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            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="PDB_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[410.0, -95.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="multiport"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant3" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[310.0, -25.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="multiport"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[465.0, 10.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="pattern" class="ptolemy.actor.parameters.PortParameter" value="INPUT_PDB">
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="replacement" class="ptolemy.actor.parameters.PortParameter" value="Input PDB file">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[380.0, 70.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TOPOLOGY_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[210.0, 40.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="multiport"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="pdb2gmx parameters" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="-f PDB_FILE -p TOPOLOGY_FILE -o GRO_FILE -ignh -ter">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[460.0, 150.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="multiport"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="pdb2gmx" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/pdb2gmx&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[665.0, -70.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <relation name="relation2" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation7" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation5" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation9" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation4" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation8_6" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation6_9" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation3_14" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation3" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation6" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <link port="gro_filename" relation="relation8_6"/>
        <link port="pdb_filename" relation="relation6_9"/>
        <link port="Output" relation="relation6"/>
        <link port="top_filename" relation="relation3_14"/>
        <link port="String Replace3.pattern" relation="relation5"/>
        <link port="String Replace3.replacement" relation="relation6_9"/>
        <link port="String Replace3.stringToEdit" relation="relation2"/>
        <link port="String Replace3.output" relation="relation3"/>
        <link port="String Constant.output" relation="relation5"/>
        <link port="String Constant3.output" relation="relation7"/>
        <link port="String Replace2.pattern" relation="relation7"/>
        <link port="String Replace2.replacement" relation="relation8_6"/>
        <link port="String Replace2.stringToEdit" relation="relation"/>
        <link port="String Replace2.output" relation="relation2"/>
        <link port="String Replace.pattern" relation="relation9"/>
        <link port="String Replace.replacement" relation="relation3_14"/>
        <link port="String Replace.stringToEdit" relation="relation4"/>
        <link port="String Replace.output" relation="relation"/>
        <link port="String Constant2.output" relation="relation9"/>
        <link port="pdb2gmx parameters.output" relation="relation4"/>
        <link port="pdb2gmx.arguments" relation="relation3"/>
        <link port="pdb2gmx.output" relation="relation6"/>
    </entity>
    <entity name="pdb2gmx output" class="ptolemy.actor.lib.gui.Display">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={857, 427, 332, 232}, maximized=false}">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[460.0, -45.0]">
        </property>
    </entity>
    <entity name="Box size (relative)" class="org.sdm.spa.StringConst">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="value" class="ptolemy.data.expr.FileParameter" value="-d 1.5">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
        </property>
        <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
        </property>
        <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
            <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
            </property>
            <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
            </property>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[-53.64583969116211, 194.6826171875]">
        </property>
        <port name="trigger" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="multiport"/>
            <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </port>
    </entity>
    <entity name="Box size (absolute)" class="org.sdm.spa.StringConst">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="value" class="ptolemy.data.expr.FileParameter" value="-box x y z">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
        </property>
        <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
        </property>
        <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
            <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
            </property>
            <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
            </property>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[-43.64583969116211, 139.6826171875]">
        </property>
        <port name="trigger" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="multiport"/>
            <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </port>
    </entity>
    <entity name="Select" class="ptolemy.actor.lib.Select">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="SelectIcon" class="ptolemy.vergil.icon.EditorIcon">
            <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds = {44, 198, 815, 509}, maximized = false}">
            </property>
            <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 400]">
            </property>
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:50:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Select">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:926:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ControlActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[81.35416030883789, 194.6826171875]">
        </property>
        <port name="control" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
            </property>
        </port>
    </entity>
    <entity name="Box size type selector" class="ptolemy.actor.lib.Expression">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="2">
            <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
            </property>
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
        </property>
        <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
            <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
            </property>
            <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
            </property>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="{-65.0, 240.0}">
        </property>
    </entity>
    <entity name="editconf output" class="ptolemy.actor.lib.gui.Display">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[460.0, 30.0]">
        </property>
    </entity>
    <entity name="editconf" class="ptolemy.actor.TypedCompositeActor">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/composite.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/composite-sm.gif</configure>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="{365.0, 30.0}">
        </property>
        <port name="port_0" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
        </port>
        <port name="port_5" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_9" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <entity name="String Constant" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[260.0, 90.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="multiport"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="editconf" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/editconf&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[585.0, 225.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[425.0, 230.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="editconf parameters" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="-f GRO_FILE -o GRO_FILE BOX_SIZE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[470.0, 90.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="multiport"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[425.0, 145.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="BOX_SIZE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[260.0, 145.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="multiport"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <relation name="relation10" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation14" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation3" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation11" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation7" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation15_0" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation12_5" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation5_9" class="ptolemy.actor.TypedIORelation">
        </relation>
        <link port="port_0" relation="relation15_0"/>
        <link port="port_5" relation="relation12_5"/>
        <link port="port_9" relation="relation5_9"/>
        <link port="String Constant.output" relation="relation7"/>
        <link port="editconf.arguments" relation="relation14"/>
        <link port="editconf.output" relation="relation15_0"/>
        <link port="String Replace2.pattern" relation="relation11"/>
        <link port="String Replace2.replacement" relation="relation12_5"/>
        <link port="String Replace2.stringToEdit" relation="relation10"/>
        <link port="String Replace2.output" relation="relation14"/>
        <link port="editconf parameters.output" relation="relation3"/>
        <link port="String Replace.pattern" relation="relation7"/>
        <link port="String Replace.replacement" relation="relation5_9"/>
        <link port="String Replace.stringToEdit" relation="relation3"/>
        <link port="String Replace.output" relation="relation10"/>
        <link port="String Constant2.output" relation="relation11"/>
    </entity>
    <entity name="genbox output" class="ptolemy.actor.lib.gui.Display">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[460.0, 110.0]">
        </property>
    </entity>
    <entity name="genbox" class="ptolemy.actor.TypedCompositeActor">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/composite.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/composite-sm.gif</configure>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[365.0, 110.0]">
        </property>
        <port name="port_1" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
        </port>
        <port name="port_6" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
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        <port name="port_11" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <entity name="String Constant" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="-cp GRO_FILE -cs -p TOP_FILE -o GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{65.0, 505.0}">
            </property>
        </entity>
        <entity name="String Constant3" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TOP_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[-20.0, 645.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="multiport"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="false">
                </property>
            </port>
        </entity>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[-5.0, 430.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="multiport"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="false">
                </property>
            </port>
        </entity>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[345.0, 590.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[260.0, 470.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="genbox" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/genbox&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[365.0, 380.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <relation name="relation4" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation3" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation7" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation11" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation10" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation14" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation5_6" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation6_11" class="ptolemy.actor.TypedIORelation">
        </relation>
        <link port="port_1" relation="relation14"/>
        <link port="port_6" relation="relation5_6"/>
        <link port="port_11" relation="relation6_11"/>
        <link port="String Constant.output" relation="relation3"/>
        <link port="String Constant3.output" relation="relation10"/>
        <link port="String Constant2.output" relation="relation4"/>
        <link port="String Replace2.pattern" relation="relation10"/>
        <link port="String Replace2.replacement" relation="relation6_11"/>
        <link port="String Replace2.stringToEdit" relation="relation7"/>
        <link port="String Replace2.output" relation="relation11"/>
        <link port="String Replace.pattern" relation="relation4"/>
        <link port="String Replace.replacement" relation="relation5_6"/>
        <link port="String Replace.stringToEdit" relation="relation3"/>
        <link port="String Replace.output" relation="relation7"/>
        <link port="genbox.arguments" relation="relation11"/>
        <link port="genbox.output" relation="relation14"/>
    </entity>
    <entity name="Positive ion" class="org.sdm.spa.StringConst">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="value" class="ptolemy.data.expr.FileParameter" value="Na+">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
        </property>
        <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
        </property>
        <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
            <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
            </property>
            <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
            </property>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="{-60.0, 345.0}">
        </property>
    </entity>
    <entity name="Number of positive ions" class="org.sdm.spa.StringConst">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="value" class="ptolemy.data.expr.FileParameter" value="1">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
        </property>
        <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
        </property>
        <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
            <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
            </property>
            <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
            </property>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="{-70.0, 385.0}">
        </property>
    </entity>
    <entity name="Negative ion" class="org.sdm.spa.StringConst">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="value" class="ptolemy.data.expr.FileParameter" value="CL-">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
        </property>
        <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
        </property>
        <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
            <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
            </property>
            <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
            </property>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[-60.0, 425.0]">
        </property>
    </entity>
    <entity name="Number of negative ions" class="org.sdm.spa.StringConst">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="value" class="ptolemy.data.expr.FileParameter" value="2">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
        </property>
        <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
        </property>
        <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
            <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
            </property>
            <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
            </property>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[-65.0, 460.0]">
        </property>
    </entity>
    <entity name="genion output" class="ptolemy.actor.lib.gui.Display">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[475.0, 285.0]">
        </property>
    </entity>
    <entity name="genion" class="ptolemy.actor.TypedCompositeActor">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/composite.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/composite-sm.gif</configure>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[375.0, 285.0]">
        </property>
        <port name="port_3" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_9" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_12" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_19" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_25" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_28" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
        </port>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[310.0, 450.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant6" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="NEG_ION_NUM">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[710.0, 345.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace4" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[590.0, 430.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant5" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="NEG_ION">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[520.0, 330.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[10.0, 435.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace5" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[725.0, 420.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="POS_ION" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="POS_ION">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[215.0, 385.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="-s em.tpr -o GRO_FILE -pname POS_ION -np POS_ION_NUM -nname NEG_ION -nn NEG_ION_NUM">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[150.0, 525.0]">
            </property>
        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[179.237060546875, 464.3798828125]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="genion" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/genion&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[315.0, 680.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace3" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[450.0, 440.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant4" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="POS_ION_NUM">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[345.0, 360.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <relation name="relation17" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation16" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation4" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation24" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation3" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation7" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation10" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation11" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation19" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation14" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation18" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation23_3" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation22_9" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation21_12" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation20_19" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation5_25" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation25_28" class="ptolemy.actor.TypedIORelation">
        </relation>
        <link port="port_3" relation="relation23_3"/>
        <link port="port_9" relation="relation22_9"/>
        <link port="port_12" relation="relation21_12"/>
        <link port="port_19" relation="relation20_19"/>
        <link port="port_25" relation="relation5_25"/>
        <link port="port_28" relation="relation25_28"/>
        <link port="String Replace2.pattern" relation="relation16"/>
        <link port="String Replace2.replacement" relation="relation20_19"/>
        <link port="String Replace2.stringToEdit" relation="relation7"/>
        <link port="String Replace2.output" relation="relation10"/>
        <link port="String Constant6.output" relation="relation19"/>
        <link port="String Replace4.pattern" relation="relation18"/>
        <link port="String Replace4.replacement" relation="relation22_9"/>
        <link port="String Replace4.stringToEdit" relation="relation11"/>
        <link port="String Replace4.output" relation="relation14"/>
        <link port="String Constant5.output" relation="relation18"/>
        <link port="String Constant2.output" relation="relation4"/>
        <link port="String Replace5.pattern" relation="relation19"/>
        <link port="String Replace5.replacement" relation="relation23_3"/>
        <link port="String Replace5.stringToEdit" relation="relation14"/>
        <link port="String Replace5.output" relation="relation24"/>
        <link port="POS_ION.output" relation="relation16"/>
        <link port="String Constant.output" relation="relation3"/>
        <link port="String Replace.pattern" relation="relation4"/>
        <link port="String Replace.replacement" relation="relation5_25"/>
        <link port="String Replace.stringToEdit" relation="relation3"/>
        <link port="String Replace.output" relation="relation7"/>
        <link port="genion.arguments" relation="relation24"/>
        <link port="genion.output" relation="relation25_28"/>
        <link port="String Replace3.pattern" relation="relation17"/>
        <link port="String Replace3.replacement" relation="relation21_12"/>
        <link port="String Replace3.stringToEdit" relation="relation10"/>
        <link port="String Replace3.output" relation="relation11"/>
        <link port="String Constant4.output" relation="relation17"/>
    </entity>
    <entity name="grompp (for genion) output" class="ptolemy.actor.lib.gui.Display">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[470.0, 200.0]">
        </property>
    </entity>
    <entity name="Energy minimisation" class="org.sdm.spa.StringConst">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="value" class="ptolemy.data.expr.FileParameter" value="em.mdp">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
        </property>
        <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
        </property>
        <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
            <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
            </property>
            <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
            </property>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[0.0, 615.0]">
        </property>
    </entity>
    <entity name="Position restraints" class="org.sdm.spa.StringConst">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="value" class="ptolemy.data.expr.FileParameter" value="pr.mdp">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
        </property>
        <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
        </property>
        <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
            <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
            </property>
            <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
            </property>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[-5.0, 665.0]">
        </property>
    </entity>
    <entity name="Molecular dynamics" class="org.sdm.spa.StringConst">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/basic-actor-sm.gif</configure>
        </property>
        <property name="value" class="ptolemy.data.expr.FileParameter" value="md.mdp">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
        </property>
        <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
        </property>
        <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
            <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
            </property>
            <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
            </property>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[0.0, 720.0]">
        </property>
    </entity>
    <entity name="grompp (for genion)" class="ptolemy.actor.TypedCompositeActor">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/composite.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/composite-sm.gif</configure>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[370.0, 200.0]">
        </property>
        <port name="port_0" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
        </port>
        <port name="port_10" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_12" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_18" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TOP_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[370.0, 610.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[230.0, 630.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant3" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="MDP_EM">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[540.0, 610.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[370.0, 685.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace3" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[520.0, 710.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="grompp (genion) parameters" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="-f MDP_EM -c GRO_FILE -o em.tpr -p TOP_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[295.0, 795.0]">
            </property>
        </entity>
        <entity name="grompp (for genion)" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/grompp&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[680.0, 680.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[225.0, 730.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <relation name="relation19" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation3" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation14" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation10" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation11" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation7" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation4" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation24" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation6_10" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation16_12" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation5_18" class="ptolemy.actor.TypedIORelation">
        </relation>
        <link port="port_0" relation="relation24"/>
        <link port="port_10" relation="relation6_10"/>
        <link port="port_12" relation="relation16_12"/>
        <link port="port_18" relation="relation5_18"/>
        <link port="String Constant2.output" relation="relation10"/>
        <link port="String Constant.output" relation="relation4"/>
        <link port="String Constant3.output" relation="relation14"/>
        <link port="String Replace2.pattern" relation="relation10"/>
        <link port="String Replace2.replacement" relation="relation6_10"/>
        <link port="String Replace2.stringToEdit" relation="relation7"/>
        <link port="String Replace2.output" relation="relation11"/>
        <link port="String Replace3.pattern" relation="relation14"/>
        <link port="String Replace3.replacement" relation="relation16_12"/>
        <link port="String Replace3.stringToEdit" relation="relation11"/>
        <link port="String Replace3.output" relation="relation19"/>
        <link port="grompp (genion) parameters.output" relation="relation3"/>
        <link port="grompp (for genion).arguments" relation="relation19"/>
        <link port="grompp (for genion).output" relation="relation24"/>
        <link port="String Replace.pattern" relation="relation4"/>
        <link port="String Replace.replacement" relation="relation5_18"/>
        <link port="String Replace.stringToEdit" relation="relation3"/>
        <link port="String Replace.output" relation="relation7"/>
    </entity>
    <entity name="grompp (em) output" class="ptolemy.actor.lib.gui.Display">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[475.0, 375.0]">
        </property>
    </entity>
    <entity name="grompp (em)" class="ptolemy.actor.TypedCompositeActor">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/composite.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/composite-sm.gif</configure>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[370.0, 385.0]">
        </property>
        <port name="port_0" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[1000.0, 520.0]">
            </property>
        </port>
        <port name="port_9" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[-5.0, 325.0]">
            </property>
        </port>
        <port name="port_17" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[-5.0, 385.0]">
            </property>
        </port>
        <port name="tpr file" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[1000.0, 580.0]">
            </property>
        </port>
        <port name="mdp_file" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[-10.0, 455.0]">
            </property>
        </port>
        <entity name="String Constant6" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".mdp">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[350.0, 705.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace5" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[536.9614562988281, 725.9701843261719]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="MDP_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[-5.0, 635.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace4" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[685.0, 645.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="grompp" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/grompp&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[805.0, 645.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant4" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TOP_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[420.0, 580.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="-f MDP_FILE -c GRO_FILE -p TOP_FILE -o TPR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[-330.0, 745.0]">
            </property>
        </entity>
        <entity name="String Constant7" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".tpr">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
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            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
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            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
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                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
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            <property name="_location" class="ptolemy.kernel.util.Location" value="{345, 725}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
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        </entity>
        <entity name="String Constant3" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
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            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
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                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
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            <property name="_location" class="ptolemy.kernel.util.Location" value="[195.0, 585.0]">
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        </entity>
        <entity name="String Replace3" class="ptolemy.actor.lib.string.StringReplace">
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                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
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                <configure>/actorthumbs/basic-actor-sm.gif</configure>
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        </entity>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
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                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
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            <property name="_location" class="ptolemy.kernel.util.Location" value="{210, 655}">
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        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
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                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
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        </entity>
        <entity name="String Constant5" class="org.sdm.spa.StringConst">
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                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
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                <configure>/actorthumbs/basic-actor-sm.gif</configure>
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            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
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            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
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                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
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            <property name="_location" class="ptolemy.kernel.util.Location" value="[635.0, 570.0]">
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            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
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        </entity>
        <relation name="relation28" class="ptolemy.actor.TypedIORelation">
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        <relation name="relation4" class="ptolemy.actor.TypedIORelation">
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        <relation name="relation14" class="ptolemy.actor.TypedIORelation">
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            </property>
        </relation>
        <relation name="relation26" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
            <vertex name="vertex1" value="[-10.0, 560.0]">
            </vertex>
        </relation>
        <relation name="relation7" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation27" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation24" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation30" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation19" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation3" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation31_0" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation6_9" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation5_17" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
            <vertex name="vertex1" value="[640.0, 720.0]">
            </vertex>
        </relation>
        <link port="port_0" relation="relation31_0"/>
        <link port="port_9" relation="relation6_9"/>
        <link port="port_17" relation="relation5_17"/>
        <link port="tpr file" relation="relation"/>
        <link port="mdp_file" relation="relation26"/>
        <link port="String Constant6.output" relation="relation27"/>
        <link port="String Replace5.pattern" relation="relation27"/>
        <link port="String Replace5.replacement" relation="relation28"/>
        <link port="String Replace5.stringToEdit" relation="relation26"/>
        <link port="String Replace5.output" relation="relation"/>
        <link port="String Constant2.output" relation="relation4"/>
        <link port="String Replace4.pattern" relation="relation24"/>
        <link port="String Replace4.replacement" relation="relation"/>
        <link port="String Replace4.stringToEdit" relation="relation19"/>
        <link port="String Replace4.output" relation="relation30"/>
        <link port="grompp.arguments" relation="relation30"/>
        <link port="grompp.output" relation="relation31_0"/>
        <link port="String Constant4.output" relation="relation14"/>
        <link port="String Constant.output" relation="relation3"/>
        <link port="String Constant7.output" relation="relation28"/>
        <link port="String Constant3.output" relation="relation11"/>
        <link port="String Replace3.pattern" relation="relation14"/>
        <link port="String Replace3.replacement" relation="relation6_9"/>
        <link port="String Replace3.stringToEdit" relation="relation10"/>
        <link port="String Replace3.output" relation="relation19"/>
        <link port="String Replace2.pattern" relation="relation11"/>
        <link port="String Replace2.replacement" relation="relation5_17"/>
        <link port="String Replace2.stringToEdit" relation="relation7"/>
        <link port="String Replace2.output" relation="relation10"/>
        <link port="String Replace.pattern" relation="relation4"/>
        <link port="String Replace.replacement" relation="relation26"/>
        <link port="String Replace.stringToEdit" relation="relation3"/>
        <link port="String Replace.output" relation="relation7"/>
        <link port="String Constant5.output" relation="relation24"/>
    </entity>
    <entity name="mdrun (em) output" class="ptolemy.actor.lib.gui.Display">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[475.0, 475.0]">
        </property>
    </entity>
    <entity name="mdrun (em)" class="ptolemy.actor.TypedCompositeActor">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/composite.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/composite-sm.gif</configure>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[375.0, 475.0]">
        </property>
        <port name="port_2" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
        </port>
        <port name="port_16" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_18" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <entity name="String Replace3" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{595, 820}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="mdrun" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/mdrun&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[715.0, 705.0]">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TPR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[245.0, 775.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant4" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".tpr">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
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            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[460.0, 675.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TRR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
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            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
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            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[420.0, 770.0]">
            </property>
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            </property>
        </entity>
        <entity name="String Constant3" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
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            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
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            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[595.0, 755.0]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant5" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".trr">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
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                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
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            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
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                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[460.0092468261719, 689.5660705566406]">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
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            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
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            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
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            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
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            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
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            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
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            </port>
        </entity>
        <entity name="String Replace4" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
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            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
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            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
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            <property name="_location" class="ptolemy.kernel.util.Location" value="[470.0, 730.0]">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
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            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
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            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
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            </port>
        </entity>
        <entity name="mdrun parameters" class="org.sdm.spa.StringConst">
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                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
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            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="-s TPR_FILE -o TRR_FILE -c GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
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            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
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            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
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            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[-5.0, 850.0]">
            </property>
        </entity>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{420, 830}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <relation name="relation14" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation28" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation7" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation3" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation27" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation26" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation24" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
            <vertex name="vertex1" value="[325.0, 740.0]">
            </vertex>
        </relation>
        <relation name="relation4" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation11" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation19" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation10" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation29_2" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation5_18" class="ptolemy.actor.TypedIORelation">
        </relation>
        <link port="port_2" relation="relation29_2"/>
        <link port="port_16" relation="relation24"/>
        <link port="port_18" relation="relation5_18"/>
        <link port="String Replace3.pattern" relation="relation19"/>
        <link port="String Replace3.replacement" relation="relation5_18"/>
        <link port="String Replace3.stringToEdit" relation="relation4"/>
        <link port="String Replace3.output" relation="relation7"/>
        <link port="mdrun.arguments" relation="relation7"/>
        <link port="mdrun.output" relation="relation29_2"/>
        <link port="String Constant.output" relation="relation11"/>
        <link port="String Constant4.output" relation="relation26"/>
        <link port="String Constant2.output" relation="relation14"/>
        <link port="String Constant3.output" relation="relation19"/>
        <link port="String Constant5.output" relation="relation27"/>
        <link port="String Replace.pattern" relation="relation11"/>
        <link port="String Replace.replacement" relation="relation24"/>
        <link port="String Replace.stringToEdit" relation="relation10"/>
        <link port="String Replace.output" relation="relation3"/>
        <link port="String Replace4.pattern" relation="relation26"/>
        <link port="String Replace4.replacement" relation="relation27"/>
        <link port="String Replace4.stringToEdit" relation="relation24"/>
        <link port="String Replace4.output" relation="relation28"/>
        <link port="mdrun parameters.output" relation="relation10"/>
        <link port="String Replace2.pattern" relation="relation14"/>
        <link port="String Replace2.replacement" relation="relation28"/>
        <link port="String Replace2.stringToEdit" relation="relation3"/>
        <link port="String Replace2.output" relation="relation4"/>
    </entity>
    <entity name="grompp (pr)" class="ptolemy.actor.TypedCompositeActor">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/composite.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/composite-sm.gif</configure>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[370.0, 580.0]">
        </property>
        <port name="port_0" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{1010.0, 530.0}">
            </property>
        </port>
        <port name="port_9" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[5.0, 290.0]">
            </property>
        </port>
        <port name="port_17" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{5.0, 395.0}">
            </property>
        </port>
        <port name="tpr file" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{1010.0, 590.0}">
            </property>
        </port>
        <port name="mdp_file" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[5.0, 460.0]">
            </property>
        </port>
        <entity name="String Constant6" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".mdp">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{360.0, 715.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace5" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{546.9614, 735.9702}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="MDP_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{5.0, 645.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace4" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{695.0, 655.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="grompp" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/grompp&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{815.0, 655.0}">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant4" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TOP_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{430.0, 590.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="-f MDP_FILE -c GRO_FILE -p TOP_FILE -o TPR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{-320.0, 755.0}">
            </property>
        </entity>
        <entity name="String Constant7" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".tpr">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{355.0, 735.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant3" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{205.0, 595.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace3" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{430.0, 645.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
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                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{220.0, 665.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{155.0, 765.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant5" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TPR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{645.0, 580.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <relation name="relation28" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation4" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation14" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation11" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation10" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation26" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
            <vertex name="vertex1" value="[-10.0, 560.0]">
            </vertex>
        </relation>
        <relation name="relation7" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation27" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation24" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation30" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation19" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation3" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation31_0" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation6_9" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation5_17" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
            <vertex name="vertex1" value="[640.0, 720.0]">
            </vertex>
        </relation>
        <link port="port_0" relation="relation31_0"/>
        <link port="port_9" relation="relation6_9"/>
        <link port="port_17" relation="relation5_17"/>
        <link port="tpr file" relation="relation"/>
        <link port="mdp_file" relation="relation26"/>
        <link port="String Constant6.output" relation="relation27"/>
        <link port="String Replace5.pattern" relation="relation27"/>
        <link port="String Replace5.replacement" relation="relation28"/>
        <link port="String Replace5.stringToEdit" relation="relation26"/>
        <link port="String Replace5.output" relation="relation"/>
        <link port="String Constant2.output" relation="relation4"/>
        <link port="String Replace4.pattern" relation="relation24"/>
        <link port="String Replace4.replacement" relation="relation"/>
        <link port="String Replace4.stringToEdit" relation="relation19"/>
        <link port="String Replace4.output" relation="relation30"/>
        <link port="grompp.arguments" relation="relation30"/>
        <link port="grompp.output" relation="relation31_0"/>
        <link port="String Constant4.output" relation="relation14"/>
        <link port="String Constant.output" relation="relation3"/>
        <link port="String Constant7.output" relation="relation28"/>
        <link port="String Constant3.output" relation="relation11"/>
        <link port="String Replace3.pattern" relation="relation14"/>
        <link port="String Replace3.replacement" relation="relation6_9"/>
        <link port="String Replace3.stringToEdit" relation="relation10"/>
        <link port="String Replace3.output" relation="relation19"/>
        <link port="String Replace2.pattern" relation="relation11"/>
        <link port="String Replace2.replacement" relation="relation5_17"/>
        <link port="String Replace2.stringToEdit" relation="relation7"/>
        <link port="String Replace2.output" relation="relation10"/>
        <link port="String Replace.pattern" relation="relation4"/>
        <link port="String Replace.replacement" relation="relation26"/>
        <link port="String Replace.stringToEdit" relation="relation3"/>
        <link port="String Replace.output" relation="relation7"/>
        <link port="String Constant5.output" relation="relation24"/>
    </entity>
    <entity name="grompp (pr) output" class="ptolemy.actor.lib.gui.Display">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[480.0, 570.0]">
        </property>
    </entity>
    <entity name="mdrun (pr) output" class="ptolemy.actor.lib.gui.Display">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[480.0, 680.0]">
        </property>
    </entity>
    <entity name="mdrun (pr)" class="ptolemy.actor.TypedCompositeActor">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/composite.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/composite-sm.gif</configure>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[375.0, 680.0]">
        </property>
        <port name="port_2" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
        </port>
        <port name="port_16" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_18" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <entity name="String Replace3" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{605.0, 830.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
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                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="mdrun" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/mdrun&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{725.0, 715.0}">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TPR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{255.0, 785.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant4" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".tpr">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{470.0, 685.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TRR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{430.0, 780.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant3" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{605.0, 765.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant5" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".trr">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{470.00925, 699.56604}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{255.0, 850.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace4" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{480.0, 740.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="mdrun parameters" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="-s TPR_FILE -o TRR_FILE -c GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{5.0, 860.0}">
            </property>
        </entity>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{430.0, 840.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <relation name="relation14" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation28" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation7" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation3" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation27" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation26" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation24" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
            <vertex name="vertex1" value="[325.0, 740.0]">
            </vertex>
        </relation>
        <relation name="relation4" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation11" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation19" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation10" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation29_2" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation5_18" class="ptolemy.actor.TypedIORelation">
        </relation>
        <link port="port_2" relation="relation29_2"/>
        <link port="port_16" relation="relation24"/>
        <link port="port_18" relation="relation5_18"/>
        <link port="String Replace3.pattern" relation="relation19"/>
        <link port="String Replace3.replacement" relation="relation5_18"/>
        <link port="String Replace3.stringToEdit" relation="relation4"/>
        <link port="String Replace3.output" relation="relation7"/>
        <link port="mdrun.arguments" relation="relation7"/>
        <link port="mdrun.output" relation="relation29_2"/>
        <link port="String Constant.output" relation="relation11"/>
        <link port="String Constant4.output" relation="relation26"/>
        <link port="String Constant2.output" relation="relation14"/>
        <link port="String Constant3.output" relation="relation19"/>
        <link port="String Constant5.output" relation="relation27"/>
        <link port="String Replace.pattern" relation="relation11"/>
        <link port="String Replace.replacement" relation="relation24"/>
        <link port="String Replace.stringToEdit" relation="relation10"/>
        <link port="String Replace.output" relation="relation3"/>
        <link port="String Replace4.pattern" relation="relation26"/>
        <link port="String Replace4.replacement" relation="relation27"/>
        <link port="String Replace4.stringToEdit" relation="relation24"/>
        <link port="String Replace4.output" relation="relation28"/>
        <link port="mdrun parameters.output" relation="relation10"/>
        <link port="String Replace2.pattern" relation="relation14"/>
        <link port="String Replace2.replacement" relation="relation28"/>
        <link port="String Replace2.stringToEdit" relation="relation3"/>
        <link port="String Replace2.output" relation="relation4"/>
    </entity>
    <entity name="grompp (md)" class="ptolemy.actor.TypedCompositeActor">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/composite.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/composite-sm.gif</configure>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[370.0, 790.0]">
        </property>
        <port name="port_0" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{1010.0, 530.0}">
            </property>
        </port>
        <port name="port_9" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{5.0, 335.0}">
            </property>
        </port>
        <port name="port_17" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{5.0, 395.0}">
            </property>
        </port>
        <port name="tpr file" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{1010.0, 590.0}">
            </property>
        </port>
        <port name="mdp_file" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
            <property name="_location" class="ptolemy.kernel.util.Location" value="[5.0, 455.0]">
            </property>
        </port>
        <entity name="String Constant6" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".mdp">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{360.0, 715.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace5" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{546.9614, 735.9702}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="MDP_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{5.0, 645.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace4" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{695.0, 655.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="grompp" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/grompp&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{815.0, 655.0}">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant4" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TOP_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{430.0, 590.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="-f MDP_FILE -c GRO_FILE -p TOP_FILE -o TPR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{-320.0, 755.0}">
            </property>
        </entity>
        <entity name="String Constant7" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".tpr">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{355.0, 735.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant3" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{205.0, 595.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Replace3" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{430.0, 645.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{220.0, 665.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{155.0, 765.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant5" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TPR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="semanticType111" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ConstantActor">
            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{645.0, 580.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <relation name="relation28" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation4" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation14" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation11" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation10" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation26" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
            <vertex name="vertex1" value="[-10.0, 560.0]">
            </vertex>
        </relation>
        <relation name="relation7" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation27" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation24" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation30" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation19" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation3" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
        </relation>
        <relation name="relation31_0" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation6_9" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation5_17" class="ptolemy.actor.TypedIORelation">
        </relation>
        <relation name="relation" class="ptolemy.actor.TypedIORelation">
            <property name="width" class="ptolemy.data.expr.Parameter" value="1">
            </property>
            <vertex name="vertex1" value="[640.0, 720.0]">
            </vertex>
        </relation>
        <link port="port_0" relation="relation31_0"/>
        <link port="port_9" relation="relation6_9"/>
        <link port="port_17" relation="relation5_17"/>
        <link port="tpr file" relation="relation"/>
        <link port="mdp_file" relation="relation26"/>
        <link port="String Constant6.output" relation="relation27"/>
        <link port="String Replace5.pattern" relation="relation27"/>
        <link port="String Replace5.replacement" relation="relation28"/>
        <link port="String Replace5.stringToEdit" relation="relation26"/>
        <link port="String Replace5.output" relation="relation"/>
        <link port="String Constant2.output" relation="relation4"/>
        <link port="String Replace4.pattern" relation="relation24"/>
        <link port="String Replace4.replacement" relation="relation"/>
        <link port="String Replace4.stringToEdit" relation="relation19"/>
        <link port="String Replace4.output" relation="relation30"/>
        <link port="grompp.arguments" relation="relation30"/>
        <link port="grompp.output" relation="relation31_0"/>
        <link port="String Constant4.output" relation="relation14"/>
        <link port="String Constant.output" relation="relation3"/>
        <link port="String Constant7.output" relation="relation28"/>
        <link port="String Constant3.output" relation="relation11"/>
        <link port="String Replace3.pattern" relation="relation14"/>
        <link port="String Replace3.replacement" relation="relation6_9"/>
        <link port="String Replace3.stringToEdit" relation="relation10"/>
        <link port="String Replace3.output" relation="relation19"/>
        <link port="String Replace2.pattern" relation="relation11"/>
        <link port="String Replace2.replacement" relation="relation5_17"/>
        <link port="String Replace2.stringToEdit" relation="relation7"/>
        <link port="String Replace2.output" relation="relation10"/>
        <link port="String Replace.pattern" relation="relation4"/>
        <link port="String Replace.replacement" relation="relation26"/>
        <link port="String Replace.stringToEdit" relation="relation3"/>
        <link port="String Replace.output" relation="relation7"/>
        <link port="String Constant5.output" relation="relation24"/>
    </entity>
    <entity name="grompp (md) output" class="ptolemy.actor.lib.gui.Display">
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            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[495.0, 780.0]">
        </property>
    </entity>
    <entity name="mdrun (md) output" class="ptolemy.actor.lib.gui.Display">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/text_disp.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/text_disp-sm.gif</configure>
        </property>
        <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
        </property>
        <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="40">
        </property>
        <property name="suppressBlankLines" class="ptolemy.data.expr.Parameter" value="false">
        </property>
        <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute">
        </property>
        <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:7:1">
        </property>
        <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.gui.Display">
            <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:883:1">
            </property>
        </property>
        <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[495.0, 895.0]">
        </property>
    </entity>
    <entity name="mdrun (md)" class="ptolemy.actor.TypedCompositeActor">
        <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>../kepler-docs/dev/usability/graphics/svg/composite.svg</configure>
        </property>
        <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
            <configure>/actorthumbs/composite-sm.gif</configure>
        </property>
        <property name="_location" class="ptolemy.kernel.util.Location" value="[370.0, 895.0]">
        </property>
        <port name="port_2" class="ptolemy.actor.TypedIOPort">
            <property name="output"/>
        </port>
        <port name="port_16" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <port name="port_18" class="ptolemy.actor.TypedIOPort">
            <property name="input"/>
        </port>
        <entity name="String Replace3" class="ptolemy.actor.lib.string.StringReplace">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="replaceAll" class="ptolemy.data.expr.Parameter" value="true">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:98:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.string.StringReplace">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:972:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{605.0, 830.0}">
            </property>
            <port name="pattern" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="replacement" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
            <port name="stringToEdit" class="ptolemy.actor.parameters.ParameterPort">
                <property name="input"/>
                <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="mdrun" class="org.sdm.spa.CommandLineExec">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/cmd.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/cmd-sm.gif</configure>
            </property>
            <property name="command" class="ptolemy.actor.parameters.PortParameter" value="&quot;C:/gromacs/bin/mdrun&quot;">
            </property>
            <property name="environment" class="ptolemy.data.expr.Parameter" value="{{name = &quot;&quot;, value = &quot;&quot;}}">
            </property>
            <property name="directory" class="ptolemy.data.expr.FileParameter" value="file:/C:/Documents%20and%20Settings/Edan/My%20Documents/Uni/Work/GROMACS/bulk_water/lac21/Kepler%20test/">
            </property>
            <property name="outputLineByLine" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="waitForProcess" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:185:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.CommandLineExec">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1040:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{725.0, 715.0}">
            </property>
            <port name="trigger" class="ptolemy.actor.TypedIOPort">
                <property name="input"/>
                <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
                </property>
            </port>
        </entity>
        <entity name="String Constant" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TPR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
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            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{255.0, 785.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant4" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".tpr">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
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            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{470.0, 685.0}">
            </property>
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        </entity>
        <entity name="String Constant2" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="TRR_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
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                </property>
            </property>
            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
            </property>
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            </property>
            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{430.0, 780.0}">
            </property>
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            </property>
        </entity>
        <entity name="String Constant3" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value="GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
            </property>
            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
                </property>
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            <property name="semanticType000" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
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            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
                <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="value">
                </property>
                <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{605.0, 765.0}">
            </property>
            <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
            </property>
        </entity>
        <entity name="String Constant5" class="org.sdm.spa.StringConst">
            <property name="_svgIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
            </property>
            <property name="_thumbnailRasterIcon" class="ptolemy.kernel.util.ConfigurableAttribute">
                <configure>/actorthumbs/basic-actor-sm.gif</configure>
            </property>
            <property name="value" class="ptolemy.data.expr.FileParameter" value=".trr">
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        </entity>
        <entity name="String Replace" class="ptolemy.actor.lib.string.StringReplace">
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                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
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                <configure>/actorthumbs/basic-actor-sm.gif</configure>
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        </entity>
        <entity name="String Replace4" class="ptolemy.actor.lib.string.StringReplace">
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                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
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                <configure>/actorthumbs/basic-actor-sm.gif</configure>
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                <property name="input"/>
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        </entity>
        <entity name="mdrun parameters" class="org.sdm.spa.StringConst">
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                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
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                <configure>/actorthumbs/basic-actor-sm.gif</configure>
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            <property name="value" class="ptolemy.data.expr.FileParameter" value="-s TPR_FILE -o TRR_FILE -c GRO_FILE">
            </property>
            <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:204:1">
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            <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.sdm.spa.StringConst">
                <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1052:1">
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            <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
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                </property>
            </property>
            <property name="_location" class="ptolemy.kernel.util.Location" value="{5.0, 860.0}">
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        </entity>
        <entity name="String Replace2" class="ptolemy.actor.lib.string.StringReplace">
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                <configure>../kepler-docs/dev/usability/graphics/svg/basic-actor.svg</configure>
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                <configure>/actorthumbs/basic-actor-sm.gif</configure>
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        </entity>
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        <relation name="relation24" class="ptolemy.actor.TypedIORelation">
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        <relation name="relation29_2" class="ptolemy.actor.TypedIORelation">
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        <relation name="relation5_18" class="ptolemy.actor.TypedIORelation">
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        <link port="port_2" relation="relation29_2"/>
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        <link port="port_18" relation="relation5_18"/>
        <link port="String Replace3.pattern" relation="relation19"/>
        <link port="String Replace3.replacement" relation="relation5_18"/>
        <link port="String Replace3.stringToEdit" relation="relation4"/>
        <link port="String Replace3.output" relation="relation7"/>
        <link port="mdrun.arguments" relation="relation7"/>
        <link port="mdrun.output" relation="relation29_2"/>
        <link port="String Constant.output" relation="relation11"/>
        <link port="String Constant4.output" relation="relation26"/>
        <link port="String Constant2.output" relation="relation14"/>
        <link port="String Constant3.output" relation="relation19"/>
        <link port="String Constant5.output" relation="relation27"/>
        <link port="String Replace.pattern" relation="relation11"/>
        <link port="String Replace.replacement" relation="relation24"/>
        <link port="String Replace.stringToEdit" relation="relation10"/>
        <link port="String Replace.output" relation="relation3"/>
        <link port="String Replace4.pattern" relation="relation26"/>
        <link port="String Replace4.replacement" relation="relation27"/>
        <link port="String Replace4.stringToEdit" relation="relation24"/>
        <link port="String Replace4.output" relation="relation28"/>
        <link port="mdrun parameters.output" relation="relation10"/>
        <link port="String Replace2.pattern" relation="relation14"/>
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        <link port="String Replace2.stringToEdit" relation="relation3"/>
        <link port="String Replace2.output" relation="relation4"/>
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        </property>
        <vertex name="vertex1" value="[290.0, -20.0]">
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    <relation name="relation6" class="ptolemy.actor.TypedIORelation">
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    </relation>
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        <property name="width" class="ptolemy.data.expr.Parameter" value="1">
        </property>
    </relation>
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        <property name="width" class="ptolemy.data.expr.Parameter" value="1">
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    </relation>
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    <relation name="relation12" class="ptolemy.actor.TypedIORelation">
    </relation>
    <relation name="relation" class="ptolemy.actor.TypedIORelation">
        <property name="width" class="ptolemy.data.expr.Parameter" value="1">
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    <relation name="relation14_1" class="ptolemy.actor.TypedIORelation">
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    <relation name="relation21" class="ptolemy.actor.TypedIORelation">
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    <relation name="relation20" class="ptolemy.actor.TypedIORelation">
    </relation>
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        <property name="width" class="ptolemy.data.expr.Parameter" value="1">
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        <vertex name="vertex1" value="[50.0, 720.0]">
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    <link port="Master GRO file.output" relation="relation5"/>
    <link port="Master topology file.output" relation="relation6"/>
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    <link port="pdb2gmx.pdb_filename" relation="relation2"/>
    <link port="pdb2gmx.Output" relation="relation"/>
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    <link port="pdb2gmx output.input" relation="relation"/>
    <link port="Box size (relative).output" relation="relation9"/>
    <link port="Box size (absolute).output" relation="relation8"/>
    <link port="Select.input" relation="relation8"/>
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    <link port="Select.output" relation="relation12"/>
    <link port="Select.control" relation="relation13"/>
    <link port="Box size type selector.output" relation="relation13"/>
    <link port="editconf output.input" relation="relation15"/>
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    <link port="Positive ion.output" relation="relation20"/>
    <link port="Number of positive ions.output" relation="relation21"/>
    <link port="Negative ion.output" relation="relation22"/>
    <link port="Number of negative ions.output" relation="relation23"/>
    <link port="genion output.input" relation="relation25"/>
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    <link port="Energy minimisation.output" relation="relation16"/>
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    <link port="Molecular dynamics.output" relation="relation17"/>
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    <link port="grompp (em).tpr file" relation="relation24_16"/>
    <link port="grompp (em).mdp_file" relation="relation16"/>
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    <link port="mdrun (em).port_16" relation="relation24_16"/>
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    <link port="grompp (pr).mdp_file" relation="relation18"/>
    <link port="grompp (pr) output.input" relation="relation3"/>
    <link port="mdrun (pr) output.input" relation="relation7"/>
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    <link port="grompp (md).port_0" relation="relation10"/>
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    <link port="grompp (md).tpr file" relation="relation11"/>
    <link port="grompp (md).mdp_file" relation="relation17"/>
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    <link port="mdrun (md) output.input" relation="relation14"/>
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    <link port="mdrun (md).port_18" relation="relation5"/>
</entity>
