Hi,
Gromacs uses a more complicated, but also more efficient way to
determine the virial.
If you write your own program, I would the much simpler direct way
of just calculating r x f in all the force loops.
Gromacs 4.0 still always uses shift vectors, but in parallel the graph is not
used.
Berk
> Date: Fri, 28 Nov 2008 15:32:55 +0800
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] How to calculate virial in gromacs-4.0?
>
> Hi all
>
> I want to do pressure coupling in my own program.
> So These days I read associated codes in Gromacs_4.0 and I find that it
> must sum the virial first. In Gromacs-3.3.3 you use the intramolecular
> shift(graph)
> to sum the virial of the covalent bonds, but in Gromacs-4.0 the graph
> variable seems to be NULL
> when run the mdrun with domain decomposition. Is it the true?
> And if it's true how do you sum the virial with the periodic boundary
> condition
> in Gromacs_4.0 with domain decomposition? Can someone explain the way of
> summing
> virial in Gromacs_4.0 in detail? Or can you recommend some resoures about
> summing the virial with
> the periodic boundary condition?
>
> Appreciate any help in advance!
>
> Best
> wishes!
>
>
> xuji
> [EMAIL PROTECTED]
> 2008-11-28
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