[gmx-users] Getting the virial for each individual atom.

Berk Hess gmx3 at hotmail.com
Mon Jan 21 18:44:02 CET 2013


The virial has no meaning per atom.
And you can't get the virial per atom out of Gromacs, it is never calculated in that way (see the manual for details).
A special local pressure version of Gromacs exists, but even there you won't get a virial per atom.



> Date: Mon, 21 Jan 2013 12:35:04 -0500
> From: zachary.marcin at wilkes.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Getting the virial for each individual atom.
> Hello,
> For the research I'm working with, I need to get the virial for each
> individual atom in the system. I've been tracing all of the calls made in
> the methods related to virials(Version 4.5.5) and this is the call stack
> that I think has what I need.
> mdrun.c -> do_md in md.c -> do_force in sim_util.c -> calcvir.c
> I have a few questions that I was wondering if anyone could answer.
> 1. In sim_util.c, there is a comment that says "Total virial computed in
> global_stat, called from do_md". I cannot find where this is called in
> do_md. Was this changed at any point and the comment was still left in the
> code?
> 2. If I change the codes in calcvir.c to find the virials for each
> individual atom, say by piping the atom numbers and forces and everything
> needed into another program so it doesn't effect the way that gromacs runs
> and will still allow everything to do what it needs, will this be screwed
> up by/screw up the domain decomposition/the mpi stuff?
> Basically, I'm looking for advice on a method to output the individual
> virials for each atom for each frame, instead of just the final output of
> the average virial on the entire system.
> Thanks,
> Zach Marcin
> Wilkes University
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