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

[Mark Abraham]

Right. Well, charge groups should be illegal :-P

Mark

On Fri, Sep 12, 2014 at 7:34 PM, Berk Hess <hess at kth.se> wrote:

>  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> 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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