[gmx-users] Re: large scale simulation?

Dommert Florian dommert at icp.uni-stuttgart.de
Sat Mar 31 14:23:20 CEST 2012

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.


> Mark 
> -- 
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Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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