[gmx-developers] Exclude specific nonbonded interactions during md rerun for Verlet
mark.j.abraham at gmail.com
Fri Sep 12 19:32:52 CEST 2014
True for the first part, but rerun does not ever need a buffer, because
neighbour search is every frame.
On Fri, Sep 12, 2014 at 7:30 PM, Berk Hess <hess at kth.se> wrote:
> 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.
> 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.
>> On 09/12/2014 04:21 PM, Berk Hess wrote:
>>> 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.
>>> 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
> Gromacs Developers mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-developers_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> or send a mail to gmx-developers-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-developers