[gmx-developers] LJ and Coloumb per atom per group

[Berk Hess]

Hi,

In Gromacs 4.0 you can set the environment variable GMX_NB_GENERIC
Then plain C loops in src/gmxlib/nonbonded/nb_generic.c will be used.
In that file you have access to the atom numbers: ii and jnr (numbering
starts at 0),
the numbers will only be correct when you are not using domain
decomposition.
And you have access to the energy group index ggid, which is gives you
the energy
group by doing ggid/ngroup and ggid%ngroup.

Berk

Pieter van 't Hof wrote:
> Sorry, I forgot to add that this concerns only the short range versions 
> of LJ and Coloumb
>
> -------- Forwarded Message --------
> From: Pieter van 't Hof <pieter.van.t.hof at logica.com>
> Reply-to: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> To: gmx-developers at gromacs.org
> Subject: [gmx-developers] LJ and Coloumb per atom per group
> Date: Tue, 28 Jul 2009 10:02:13 +0200
>
> Hello,
>
> I would like to know where the LJ interaction is calculated (separately
> 6 and 12 if possible) and coloumb forces per atom.
>
> The idea is to generate an overview of the per-atom LJ and Coloumb
> forces per energy group (So, for example, knowing of each atom in the
> Ligand what its LJ6, LJ12 and CLB values are)
>
> I am a experienced programmer, but quite new in the architecture of
> Gromacs. A short hint to the correct place of calculation (and
> preferably where additional atom information (such as number and group)
> is available) should be enough :)
>
> Thanks in advantage
>
> Pieter 
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