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

[Berk Hess]

Hi,

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.

Cheers,

Berk

----------------------------------------
> 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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