VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat May 26 2012 - 16:19:26 CDT

On Sat, May 26, 2012 at 1:20 PM, Andrew DeYoung <adeyoung_at_andrew.cmu.edu> wrote:
> 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?

yes and no. VMD can only show what it knows about.
http://www.ks.uiuc.edu/Research/vmd/plugins/dipwatch/

you can provide partial charges via a .psf file or a .pqr file
or some similar file format or from a Tcl script.

axel.

> 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
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.