[gmx-developers] MC with PME

[David van der Spoel]

On 2010-06-14 21.09, André Assunção S. T. Ribeiro wrote:
> Dear all,
>
> I have been working to implement a Monte Carlo "integrator" for GROMACS.
> For the last couple of months I've been trying to improve performance of
> the algorithm. For that end, I have made adaptations to the ns and force
> evaluation routines. Energies for each interaction are stored
> separately, so one can just calculate the needed energy terms in each
> trial move. When treating nonbonded interactions with a cutoff, MC
> performance is more than 10-fold greater than MD for a simple system
> containing 216 SPC waters (by performance I mean number of simulation
> steps/CPU time, not actual sampling efficiency). When I use PME, the
> situation is far worst, with an approximate 3-fold increase. When I try
> to call gmx_pme_do for only a small number of atoms performance
> decreases when compared to the total calculation. For simple Ewald sum,
> there is a 10-fold increase when a single molecule is calculated,
> however, it is still a lot slower than the worst PME result. Would
> anyone have any ideas on how to increase performance here?
If you use MC you do not need to evaluate forces, this will remove 30% 
of the PME time roughly. It used to be coded in there at some stage, but 
it might have been removed.

>
> Cheers,
> Andre.
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se