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.
Mark
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