[gmx-users] How to calculate virial in gromacs-4.0?

Berk Hess gmx3 at hotmail.com
Fri Nov 28 16:23:52 CET 2008


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.


> Date: Fri, 28 Nov 2008 15:32:55 +0800
> From: xuji at home.ipe.ac.cn
> To: gmx-users at 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
>         xuji at home.ipe.ac.cn
>           2008-11-28

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