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

[Marcin, Zachary]

Tim,
The PBC's were turned off and need to be for what we're trying to do.
Pretty much everything that might work, as far as I've seen, can't unless
we change some source code to do what we need.
Thanks,
Zach

On Mon, Jan 21, 2013 at 4:47 PM, Timothy Sirk <tsirk at vt.edu> wrote:

> Zach,
>
> Do you have periodic system with charges? For PBC, you might try one of the
> forms in J. Chem. Phys. 131 154107 (2009). Electrostatics are more work...
> For Ewald sum and PPPM contribution, you could check refs in
> lammps.sandia.gov/doc/PDF/kspace.pdf
>
> We have an upcoming paper that explains in more detail how to do this with
> PPPM and gives an example with heat flux. Maybe something similar could be
> done in GROMACS with PME.
>
> best,
>
> Tim
>
>
> On Mon, Jan 21, 2013 at 1:06 PM, Marcin, Zachary
> <zachary.marcin at wilkes.edu>wrote:
>
> > 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
> > > > --
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