[gmx-developers] distance restraints and domain decomposition

Berk Hess hess at kth.se
Thu Jun 7 09:51:25 CEST 2018


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.



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

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