VMD-L Mailing List

From: Andrew DeYoung (adeyoung_at_andrew.cmu.edu)
Date: Sat May 26 2012 - 12:20:09 CDT

Hi,

I am running VMD 1.9 on Windows. I have loaded a .g96 (Gromacs)
configuration into VMD. After this, I load (into the same molecule) a .xtc
(Gromacs) trajectory. I would like to visualize the dipole moment of my
system. To try to do this, I go to:

Extensions -> Visualization -> Dipole Moment Watcher

I select the checkbox next to "Dipole 0" and then click the "Write" button
to save a .dat file. When I open the .dat file in a text editor, I see this
output:

# frame dip_x dip_y dip_z |dip|
0 0.0 0.0 0.0 0.0
1 0.0 0.0 0.0 0.0
2 0.0 0.0 0.0 0.0
3 0.0 0.0 0.0 0.0
4 0.0 0.0 0.0 0.0
5 0.0 0.0 0.0 0.0
...

And all frame numbers have "0.0 0.0 0.0 0.0" next to them, suggesting
that my system has exactly zero dipole moment at all times; however, this is
clearly not true.

I think that this error arises from the fact that .g96 configuration files
only contain atomic positions and velocities, not charges. Also, I do not
think that .xtc trajectories contain charges, either. Does this mean that I
need to switch to configuration/trajectory formats that include charges?
However, I am not sure what this would be with Gromacs, since I think that
in Gromacs, charge information is stored in topology files, not
configuration or trajectory files. Do you have any suggestions?

Thank you very much for your time!

Andrew DeYoung
Carnegie Mellon University