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

Bernd Doser bernd.doser at h-its.org
Fri Sep 12 21:13:43 CEST 2014

Hi Berk, Hi Mark,

thanks for the interesting suggestion. I will try it. However, what do
you think about my first idea, to extent the topology list, which will
be also excluded as nonbonded interactions?


On 12.09.2014 19:30, Berk Hess 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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