[gmx-developers] Exclude specific nonbonded interactions during md rerun for Verlet

[Berk Hess]

No, with charge groups you do need a buffer, grompp will even warn you 
about this.

Berk

On 09/12/2014 07:32 PM, Mark Abraham wrote:
> True for the first part, but rerun does not ever need a buffer, 
> because neighbour search is every frame.
>
> Mark
>
> On Fri, Sep 12, 2014 at 7:30 PM, Berk Hess <hess at kth.se 
> <mailto:hess at kth.se>> wrote:
>
>     Hi,
>
>     You can use the group scheme for the rerun only. If you use the
>     same potential modifiers and add a buffer to rlist, you should get
>     exactly the same answer as the Verlet scheme.
>
>     We should come up with a way to do this with the Verlet scheme
>     when we remove the group scheme.
>
>     Cheers,
>
>     Berk
>
>
>     On 09/12/2014 05:20 PM, Bernd Doser wrote:
>
>         Hi Berk,
>
>         thanks for your answer. We store force contributions between
>         two atoms
>         to analyze them. This storage will be performed during a
>         rerun. We want
>         to exclude the unneeded interactions to speed-up the rerun,
>         since we are
>         only interested in forces between two atom groups.
>
>         Cheers,
>         Bernd
>
>         On 09/12/2014 04:21 PM, Berk Hess wrote:
>
>             Hi,
>
>             Why do you need to exclude energy group interactions
>             during rerun?
>             Since you will have all the energy group pair
>             contributions you can
>             manually subtract the terms you want to exclude. You
>             wouldn't even need
>             a rerun for that if you used the energy groups for the
>             production run.
>
>             Cheers,
>
>             Berk
>
>             On 09/12/2014 03:26 PM, Bernd Doser wrote:
>
>                 Dear GROMACS developers,
>
>                 As the energy group exclusions are not implemented for
>                 the Verlet cutoff
>                 scheme, I am search for a alternative possibility to
>                 exclude specific
>                 nonbonded interactions during an md rerun.
>
>                 One idea is to use the topology exclusion list. The
>                 top->excl arrays
>                 could be modified for example at the beginning of
>                 do_force() in
>                 sim_util.c. I have tested it for a small protein and a
>                 water dimer and
>                 it works. Is there any problem doing this for more
>                 complex structures or
>                 have anyone a better idea to exclude nonbonded
>                 interactions to reduce
>                 computation time?
>
>                 Thank you very much in advance!
>
>                 Best regards,
>                 Bernd Doser
>
>
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