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

[Marcin, Zachary]

Berk,
Here is where I think I might be able to:
In calcvir.c there is a method called calc_vir which takes, among other
things, int nxf(no idea what this does), rvec x[], and revec f[].  It then
does dvxx+= x[i][xx] *f[i][XX];.
This is the same as the formula that I am trying to solve for (Vi*Pi +
.5*SUM(Rij * Fij)).
What I figured I could do is create another array to calculate the virials
for, thus giving me an index position per atom, and then use that somehow.

I also know that I can use R(ij) * F(ij), or the distance between atoms i
and j times the Forces between atoms i and j.  If anyone has any insight on
getting these, that could also work.
I know how to get the individual positions, but I don't know how I would go
about the forces aspect of that.

Thanks,
Zach

On Mon, Jan 21, 2013 at 12:44 PM, Berk Hess <gmx3 at hotmail.com> wrote:

>
> 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
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>                                           --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>