[gmx-developers] Question on P-LINCS
hess at kth.se
Tue Feb 12 16:41:39 CET 2013
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
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
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.
> 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
>>>> an efficient scalling in the parallel run of P-LINCS (perhaps there
>>>> 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.
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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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