[gmx-users] restraints between two different molecules

Mark Abraham mark.j.abraham at gmail.com
Wed May 25 16:19:38 CEST 2016


On Wed, May 25, 2016 at 4:11 PM Rebeca García Fandiño <regafan at hotmail.com>

> Dear Gromacs users,
> I am trying to apply some distance restraints between two different
> molecules in a Gromacs simulation. I have read different things in the
> Gromacs list, such as both molecules should be in the same [atomtype]
> section (which is not the case)

In old versions, it is necessary to have such restraints within the same
moleculetype (not atomype, of course). This was because the system is built
from x copies of each moleculetype.

and also something related to the use of "pull_ngroups = 2". But it is not
> clear to me, and I don´t know how could I do it, even if this is possible.
> So, the question is...would it be possible to apply restraints between
> diferent molecules during a simulation?

GROMACS 5.1 introduces an [intermolecular_interactions] that precisely
addresses this issue without needing changes to [moleculetypes] or the use
of the pull code. Please see the documentaioin for details. :-)


Any help would be appreciated.
> Best wishes,
> Dr. Rebeca Garcia
> Santiago de Compostela University
> Spain
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