[gmx-developers] distance restraints and domain decomposition

[Berk Hess]

Hi,

I filed a redmine issue: https://redmine.gromacs.org/issues/2549

Cheers,

Berk

On 2018-06-07 09:51, Berk Hess wrote:
> Hi,
>
> This is a complicated case. You have multiple monomers that are only 
> linked by distance restraints. Some of these restraints work over more 
> than half the box length. These interactions cause parts of monomers 
> to be shifted by a box vector in the shift code. This is obviously 
> incorrect. This can affect more things than the DD distance 
> calculation that you report, e.g. analysis tools.
> This is not easy to fix, one could image that all distance restraints 
> are at distances of more than half the box length. The least we should 
> do is detect such inconsistencies and generate a fatal error.
> I was about to say that you could use multiple molecule types and 
> intermolecular interactions, but could cause incorrect distances to be 
> used for the restraints.
> The only proper solution is to add some kind of proximity interaction 
> the user can specify to tell what part of the monomers are close, such 
> that GROMACS can set up the correct PBC.
>
> Cheers,
>
> Berk
>
>
> On 06/07/2018 08:42 AM, Berk Hess wrote:
>> Hi,
>>
>> The code takes PBC into account, both for intra- and intermolecular 
>> interactions.
>>
>> Could you provide me with the input to grompp?
>>
>> Cheers,
>>
>> Berk
>>
>> On 06/07/2018 08:37 AM, Kutzner, Carsten wrote:
>>>
>>>> On 7. Jun 2018, at 07:02, David van der Spoel 
>>>> <spoel at xray.bmc.uu.se> wrote:
>>>>
>>>> Den 2018-06-06 kl. 15:07, skrev Kutzner, Carsten:
>>>>> Dear developers,
>>>>> we have a ~ 40,000 atom MD system with distance restraints (bond 
>>>>> type 6)
>>>>> that does not want to run in parallel, although I assume it should.
>>>>> It runs fine without DD, e.g. -ntmpi 1 -ntomp 20, however with DD the
>>>>> following happens:
>>>>> mdrun -ntmpi 2
>>>>> Fatal error:
>>>>> There is no domain decomposition for 2 ranks that is compatible 
>>>>> with the given
>>>>> box and a minimum cell size of 11.4939 nm
>>>>> The maximum distance restraint distance is however at 4.0 nm, so 
>>>>> 11.49 nm as
>>>>> reported cannot be true, unless the PBC distance is not taken 
>>>>> properly
>>>>> into account. Is this the expected behaviour or worth generating a 
>>>>> redmine
>>>>> issue?
>>>>> Thanks,
>>>>>   Carsten
>>>> Which version?
>>> 2018
>>>
>>>> It should work with OpenMP anyway.
>>> Yes, that works, however we might want to use multiple nodes and/or 
>>> multiple
>>> GPUs for similar setups in the future.
>>>
>>> Carsten
>>>
>>>> -- 
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>> http://www.icm.uu.se
>>>> -- 
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>>> -- 
>>> Dr. Carsten Kutzner
>>> Max Planck Institute for Biophysical Chemistry
>>> Theoretical and Computational Biophysics
>>> Am Fassberg 11, 37077 Goettingen, Germany
>>> Tel. +49-551-2012313, Fax: +49-551-2012302
>>> http://www.mpibpc.mpg.de/grubmueller/kutzner
>>> http://www.mpibpc.mpg.de/grubmueller/sppexa
>>>
>>
>