[gmx-developers] distance restraints and domain decomposition

Thu Jun 7 16:02:36 CEST 2018

OK but either way if the wrong image is taken I'd expect the involved distances 
to be miles away from the reference distance, leading to large energies and 
forces and thus likely instabilities, given the force constant of 1000 
kJ/mol/nm^2 we use. Again, no sign of these so far.

But I take your point that we may start thinking of alternative ways to achieve 
the desired structural effect.

cheers

Bert

On 06/07/18 15:51, Berk Hess wrote:
> Not if the wrong image is used consistently, which is not unlikely, since a 
> large complex rotates rather slowly.
>
> Berk
>
> On 06/07/2018 03:49 PM, Bert de Groot wrote:
>> Hi,
>>
>> right, but this would be expected to lead to jumps in the restraint energies, 
>> right? So far there are no signs of these.
>>
>> cheers
>>
>> Bert
>>
>> On 06/07/18 14:08, Berk Hess wrote:
>>> Hi,
>>>
>>> But OpenMP runs could be incorrect when the restraint distance can pick up 
>>> the wrong PBC image.
>>>
>>> Cheers,
>>>
>>> Berk
>>>
>>> On 2018-06-07 14:06, Bert de Groot wrote:
>>>> Hi,
>>>>
>>>> OK, thanks, that sounds reasonable. It is admittedly a somewhat unusual 
>>>> setup, but as the openMP jobs ran without issues, the problems with the MPI 
>>>> jobs surprised us.
>>>> The system is small enough that we can use openMP nodes as workaround for now.
>>>>
>>>> The anticipated issues with analysis tools/trjconv have indeed showed up as 
>>>> well (inconsistent shift warnings), but there they can be resolved by 
>>>> feeding a tpr without the distance restraints.
>>>>
>>>> cheers
>>>>
>>>> Bert
>>>>
>>>> On 06/07/18 13:29, Berk Hess wrote:
>>>>> Hi,
>>>>>
>>>>> I "resolved" this by adding a fatal error. The error message says that the 
>>>>> only solution is increasing the box size.
>>>>> For special cases one could do better by introducing special interations 
>>>>> that would only link monomers together. But here you actually have 
>>>>> interactions that a longer than half the box size. Theoretically one could 
>>>>> also support this, but that gets complicated and bug-prone.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Berk
>>>>>
>>>>> On 2018-06-07 10:22, Berk Hess wrote:
>>>>>> 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
>>>>>>>>>> -- 
>>>>>>>>>> Gromacs Developers mailing list
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at 
>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List 
>>>>>>>>>> before posting!
>>>>>>>>>>
>>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>>
>>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers 
>>>>>>>>>> or send a mail to gmx-developers-request at gromacs.org.
>>>>>>>>> -- 
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>