[gmx-developers] Question on P-LINCS
Berk Hess
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
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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