[gmx-developers] Question on P-LINCS
k.a.feenstra at vu.nl
Thu Feb 7 14:10:47 CET 2013
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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1081 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "You Will Be Surprised At What Resides In Your |
| | Inside" (Arrested Development) |
More information about the gromacs.org_gmx-developers