3D Visualization of electric fields of charges from Gromacs
Tyrone Curtis and Edan Scriven
GromacsFieldLines.nb
- Mathematica notebook
Gromacs.m
- Package for importing Gromacs data files
Sample Gromacs data files
elac21.top - Gromacs topology file
- a plain text file containing atomic mass, charge and bonding
information for the charges in lac21 molecule
test.gro
- Gromacs export file - contains lac21 charge coordinates and
velocities
Summary of notebook contents
This Mathematica notebook is
essentially the 3DPointCharges
notebook, with an extra section at the beginning for importing data
generated by Gromacs. Please
note that this notebook has
been created using Mathematica Version 5.1. As such there may
be incompatibilities with earlier versions of Mathematica.
The molecule modelled in this notebook
is Lac21, a fragment of the lac repressor protein. Data was
obtained from Adam Fairley's Mathematics Honours thesis entitled
"Molecular Dynamics Simulations of the Self-Assembly of the Lac21 and
Lac28 peptides for Bio-Nano Applications" completed in partnership with
Dr. Anton Middelberg of the Australian
Institute for Bioengineering & Nanotechnology. An
electronic copy of this thesis may be downloaded here.
This notebook makes use of data
generated by Gromacs, a suite of
molecular dynamics tools used to perform simulations of chemical
systems at the molecular level. This
notebook requires the Gromacs.m
package, which contains commands required to import data from the
Gromacs topology and export files. The sample Gromacs files
given above may be used to test that the notebook is working
correctly and that the Gromacs package has been loaded correctly.
Detailed instructions on how to load these files are given in the
GromacsFieldLines notebook.
For more information about how the
field lines are generated once the data is imported, see the
3DPointCharges page. The
GromacsFieldLines notebook is heavily commented as well, hopefully
the instructions are easy to understand.
This notebook allows
you to plot the electric field lines for small sections of a molecule
imported from Gromacs, or the whole molecule.
Figures 1
shows just the atoms and bonds for the first 35 atoms (corresponding
to the first 3 amino acids) of Lac21. Neutral
charges are shown in green, negative charges in red and positive
charges in blue.
Figure
1 - First 3 amino acids of lac21 molecule
Figure 2 shows the field lines for the first 3 amino acids.
Figure
2 - Field lines for the first 3 amino acids of lac21 molecule
Figures 3 and 4 show the entire molecule and its
field lines.
Figure
3 - lac21 molecule
Figure
4 - lac21 field lines
The field lines plotted in Figure 4 took around 20 minutes to calculate
using the
method discussed in 3DPointCharges on a
dual processor Mac G5.
As in 3DPointCharges
there is an option for generating an animation of the field lines so
that you get a 360º view of the system - this uses the SpinShow
command in Mathematica. Note that for very complicated systems
such as that shown in figure 4, it can take a few seconds to rerender
the graphics for each viewpoint. It is also possible in
Mathematica to specify the angle at which to view the system.
As you can see from Figure 4 it is quite hard to distinguish anything
at an atomic
level, however this may be useful for viewing the electrical
properties of the molecule as a whole. At the very least it
provides a starting point for anyone interested in continuing the
study of this and other molecules using Gromacs.