VMD-L Mailing List

From: Davide Mercadante (as126_at_uni-heidelberg.de)
Date: Fri Jan 29 2016 - 03:48:55 CST

Hello John,

Thanks a lot for the reply. It would be great to have this functionality added to the plugin. I have provided sample files in the .gro and .trr format that can be downloaded here: https://www.dropbox.com/s/djlv1kzkt3725rw/sample_trajectories.tar.gz?dl=0

The files only contain two frames for testing purposes. The velocities in the .gro file are stored in the columns number 6, 7 and 8 (counting from 0). It would be great to somehow have VMD storing these information and being able to call them with the already present function "get {vx vy vz}”.

Looking forward to a reply and thanks a lot for the effort!
Davide

> On 29/01/2016, at 4:57 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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/