[gmx-developers] Question on P-LINCS

risueno at physik.hu-berlin.de risueno at physik.hu-berlin.de
Tue Feb 12 16:07:44 CET 2013

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 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?

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).

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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