[gmx-users] exclude pairs from nb pairlist

Pedro Alexandre Lapido Loureiro paloureiro at biof.ufrj.br
Fri Nov 22 14:48:46 CET 2002

Citando quantix1 at gmx.de:

> Dear Gromacs users,
> I'm wondering if it is possible to exclude certain atom pairs from
> the nonbonded pairlist or even to predefine a pairlist by hand
> and let gromacs (mdrun) use it instead of the one which is
> created internally.
> It is just for a simple md run in gas phase.
> Has anybody done something like this? If there is a simple
> way to achieve that, I'd really like to know.
> Thanks,
> Uwe

you can use an [exclusions] item in your molecule.itp or .top file or you can
create groups (energy monitor groups) and exclude all nb interactions between
them in the molecule.mdp file.


Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

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