About VMD
VMD is designed for the visualization and analysis of biological
systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.
It may be used to view more general molecules, as VMD can read standard
Protein Data Bank (PDB) files and display the contained structure. VMD
provides a wide variety of methods for rendering and coloring a
molecule: simple points and lines, CPK spheres and cylinders, licorice
bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD
can be used to animate and analyze the trajectory of a molecular
dynamics (MD) simulation. In particular, VMD can act as a graphical
front end for an external MD program by displaying and animating a
molecule undergoing simulation on a remote computer.
(description copied from vmd's
website)
VMD_AG and SharedVmd
VMD_AG is a modified version of VMD 1.8.3, which allows users to run VMD within an Access Grid session.
To work over Access Grid, VMD_AG must be used with the Access Grid shared application "SharedVmd".
VMD_AG can be also used "normally" i.e. not as an Access Grid shared application. The changes to VMD_AG merely provide additional functionality to to work together with the SharedVmd shared application.
Available Download
Installation Instructions and Notes
Before installing SharedVmd on your system, see the requirements page for vmd. It should be very useful to see the installation page to since the installation process can be very complex depending on your system and the libraries you need.At this stage you can run VMD_AG from the command line with:
If vmd is already installed on your system, this new installation won't erase the old one.
Now, to use VMD_AG over Access Grid, install the downloaded SharedVmd AG shared application package with the command:
Once SharedVmd and vmd_AG has been installed, you can use it over Access Grid just as you use the "normal vmd".
One main difference between vmd and vmd_AG is for file loading. If a
file is loaded using the "File" menu of vmd, the file will be
loaded locally and this will not be reported to other users in the
session.
To do so use the "File -> Open" menu of SharedVmd, select a file wich is present in the Venue, and if you're the leader the file will be downloaded and loaded for every users in the session:
Loading a file from SharedVmd
Known Issues
- The shared application does not synchronise with other instance when joining a session;
- Fonctionality in the "Graphics" menu doesn't work yet.
Acknowledgements
Created by Stéphane BIDET <s.bidet at uq.edu.au> (or: <stephane.bidet at tremplin-utc.net>)Funding through UQVislab and QPSF.
Any comments, suggestions to Chris Willing <c.willing at uq.edu.au>