VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 28 2016 - 21:57:04 CST

Hi,
  At present the VMD Gromacs plugin doesn't read velocities, but if you have
some sample files we could use for testing, it might only require a minor
change to add this capability. When the code was originally written, the
versions of VMD at that time didn't support velocities, but the current
versions do.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 28, 2016 at 05:30:47PM +0100, Davide Mercadante wrote:
> Dear All,
>
> I have been reading several posts about this but I couldn???t find an answer and what I am trying is not working. I have a simulation run with GROMACS and trr or eventually gro files in which velocity information for each atom are stored. In order to do something with those in my script I want to extract these information.
> I???ve found this http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/trrplugin.html which makes me think that may be there is no easy solution yet for this inside vmd. The "$sel get {vx vy vz}" command doesn???t seem to be working as I get a list with 0 values {0.0 0.0 0.0}. Looking at previous posts on the mailing list some other users successfully ran this command to get velocities out but I am not sure if they were using NAMD- or LAMMPS-like trajectories (not specified). Is there any other way of getting these information using VMD and gromacs trajectories?
>
> Thank you for your time.
>
> Cheers,
> Davide 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/