[gmx-users] Any way to not compute certain interactions?

[Mark Abraham]

Hi,

It can be tough to find concepts in large amounts of documentation when
you're guessing what names they might be using. Energy group exclusions are
definitely the way forward, however. Though I haven't tried them with the
Verlet scheme ever, and they are unlikely to have a GPU implementation.

Manually generating intermolecular interactions that are pairwise
exclusions is another option.

Mark

On Thu, 3 Mar 2016 20:39 André Farias de Moura <moura at ufscar.br> wrote:

> you should read the manual thoroughly before asking, you could have found
> on your own an mdp option that does just that: energygrp-excl
>
> On Thu, Mar 3, 2016 at 12:57 PM, Kyle Huston <khuston at umich.edu> wrote:
>
> > Hi Gromacs users,
> >
> > I'm using stochastic dynamics, and I am simulating a chain molecule near
> a
> > wall made of frozen beads. Since the wall beads are numerous and frozen,
> I
> > would prefer if Gromacs did not compute neighbor lists and forces between
> > them (I can see this is taking the most time), but I don't see any
> obvious
> > way to "turn off" their interactions in a way that boosts performance.
> >
> > Freezing the wall beads does not improve the performance versus using
> > harmonic restraints.
> >
> > Is this possible with Gromacs?
> >
> > Thanks!
> > Kyle
> >
> >
> > --
> > Kyle J. Huston
> > PhD Candidate, Chemical Engineering
> > University of Michigan
> > --
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>
> --
> _____________
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
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