[gmx-users] Re: large scale simulation?
dommert at icp.uni-stuttgart.de
Sat Mar 31 14:27:44 CEST 2012
On Sat, 2012-03-31 at 14:23 +0200, Dommert Florian wrote:
> 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
Sorry that's an error.
> for odd
I meant for even interpolation orders.
> interpolation orders.
> > Mark
> > --
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Dipl. - Phys.
Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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