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

Berk Hess hess at kth.se
Fri Sep 12 19:30:42 CEST 2014


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.
> 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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