On Sat, 2012-03-31 at 15:46 +1100, Mark Abraham wrote: > On 31/03/2012 3:40 PM, Albert wrote: > > Hi guys: > > > > thank you very much for your kind comments. Probably the most > > effective way is to optimize PME balance as Mark mentioned. It > > seems that Mark's methods improved much much better for the speed. > > If possible, could Mark share your experience how did you optimize > > the PME balance in Gromacs? Probably each of us can learn a lot from > > you. > > Shameless plug: http://dx.doi.org/10.1021/ct800016r > > The simulations to which I referred earlier did best with 1:1 PME:PP > because of the nature of the hardware. > > In practice, you can likely do pretty well with Carsten's g_tune_pme > in the GROMACS tool set. >
And a further tool is available, that calculates the error introduced by SPME. It is called g_pme_error and MPI-enabled. In combination with Carsten's tool you can tune your accuracy and speed of calculations. However, be aware that the error estimate only holds for odd interpolation orders. /Flo > Mark > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: [email protected] Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
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