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

Berk Hess hess at kth.se
Fri Sep 12 21:35:15 CEST 2014


But topology exclusions can only be applied within, not between molecules.
If you really want the force between two atoms only, you can calculate 
the distance and manually calculate the force.
You can also convert the trajectory to two atoms only and make a 
topology for the two atoms and rerun with that.



On 09/12/2014 09:13 PM, Bernd Doser wrote:
> 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?
> Cheers,
> Bernd
> 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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