[gmx-users] Any way to not compute certain interactions?
mark.j.abraham at gmail.com
Thu Mar 3 22:23:13 CET 2016
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.
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
> > wall made of frozen beads. Since the wall beads are numerous and frozen,
> > 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
> > 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
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