[gmx-users] Re: large scale simulation?

Dommert Florian 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.

/Flo

> interpolation orders.
> 
> /Flo
> 
> 
> > 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

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