[gmx-developers] Question on P-LINCS

[risueno at physik.hu-berlin.de]

Dear Berk

Thank you very much for your clarifying answers.

Best regards



> On 2/12/13 16:07 , risueno at physik.hu-berlin.de wrote:
>> Dear Gromacs developers
>>
>> Thank you very much for the replies. More concretely, could you explain
>> me
>> how are exactly the sparsity limitations for constraints on bond angles?
>> Is it possible to impose constraints on different bond angles sharing an
>> atom? For example, to impose constraints for all the hydrogen bond
>> angles
>> of Methylamine. In addition, would it be possible to constrain all bond
>> angles of heavy atoms?
> I think you can angle constrain butane, but not pentane. Then you get
> eigenvalues
> larger than 1.
>> I guess there is not any implementation of constraints on dihedral
>> angles
>> (either principal or phase dihedrals). Is this correct? Do you know if
>> any
>> popular package offers this possibility?
> There is not much point. If you want to constrain everything, using
> rigid body
> dynamics is far simpler and far more efficient. But this is not a
> popular use case.
>>
>> Berk just explained that "Constraints only contribute a small fraction
>> of
>> the total computational cost". Could you tell me how much is it
>> typically?
>> I read that it is often about 15% (for serial calculations).
> For serial it is usually between 5 and 10%. In parallel it might be more.
>
> Cheers,
>
> Berk
>>
>> Thank you very much
>>
>>
>>
>>> On 02/07/2013 02:10 PM, Anton Feenstra wrote:
>>>> On 05/02/13 17:40, risueno at physik.hu-berlin.de wrote:
>>>>> Dear Gromacs developers
>>>>>
>>>>> In the P-LINCS paper (http://pubs.acs.org/doi/abs/10.1021/ct700200b)
>>>>> it is
>>>>> stated that P-LINCS can constrain bond angles. However, in the
>>>>> Gromacs
>>>>> manual (http://www.gromacs.org/Documentation/Manual, page 181), I
>>>>> find
>>>>> that P-LINCS is used when there is domain decomposition, but that it
>>>>> "should not be used with coupled angle constraints". So I wonder, is
>>>>> it
>>>>> possible to use P-LINCS with bond angle constraints? If not, why?
>>>> The key word here is 'coupled'. P-LINCS works with angle constraints,
>>>> but not with *coupled* angle constraints. The reason is that the
>>>> approximation for the matrix inversion assumes a sparse constraints
>>>> matrix. Having coupled angle constraints breaks this sparsity
>>>> assumption. (FYI, coupled angle constriants means one has, e.g. four
>>>> atoms with 5 constraints; three for the bonds (like, i-j, j-k and k-l)
>>>> and two for the angles (i-k and j-l)).
>>>>
>>>>> In addition, I would like to ask what is the maximum number of cores
>>>>> for
>>>>> an efficient scalling in the parallel run of P-LINCS (perhaps there
>>>>> exists
>>>>> some benchmark as a function of the total number of constraints).
>>>> I don't know that. Berk is the (P-)LINCS expert.
>>>>
>>> This is usually not the right question to ask.
>>> Constraints only contribute a small fraction of the total computational
>>> cost, so the answer depends a lot on how much other work you have.
>>> Basically P-LINCS scales ok until your spatial domains get smaller than
>>> the extent of the connected constraints considered in P-LINCS,
>>> which is anyhow a hard limit on the scaling.
>>>
>>> Cheers,
>>>
>>> Berk
>>> --
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>>
>> --
>>
>> Dr. Pablo Garcia Risueño, Humboldt-Universität zu Berlin
>> Institut für Physik und IRIS Adlershof, Theoretische Festkörperphysik
>> Zum Grossen Windkanal 6, 12489 Berlin, Germany
>>
>
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--

Dr. Pablo Garcia Risueño, Humboldt-Universität zu Berlin
Institut für Physik und IRIS Adlershof, Theoretische Festkörperphysik
Zum Grossen Windkanal 6, 12489 Berlin, Germany