[gmx-users] PME problems
ckutzne at gwdg.de
Mon Aug 31 14:06:09 CEST 2009
there is nothing wrong with your parameters, the note just refers to
the direct:reciprocal workload being not optimal from a performance
point of view. With a small cutoff and a fine PME grid you will have
a high workload for the reciprocal space calculations - which is ok
and will yield correct results. However, it will not scale very well
to many cores. If you choose a larger value for rvdw, rlist and rcoulomb
and at the same time a larger value for fourierspacing, the scaling
will be better. You can manually multiply the cutoff radii and the
fourierspacing by a (small) factor and reach similar accuracy
while at the same time enabling better scaling.
You can also use the tool g_tune_pme for that, a version for
gmx 4.0.x is available here:
On Aug 31, 2009, at 1:51 PM, 秦光荣 wrote:
> I am now using Gromacs4 to deal with a membrane protein and I
> am confused on one NOTE.
> When I use the parameters "rvdw = 0.9 , rlist = 0.9,
> rcoulomb = 0.9, fourierspacing = 0.12" at the same time, a NOTE will
> come out, which is "The optimal PME mesh load for parallel
> simulation is below 0.5 and for highly parallel simulations between
> 0.25 and 0.33, for higher performance, increase the cut-off and the
> PME grid spacing".
> If I change the fourierspacing to 0.3, this note will dismiss.
> Also, if I alter the other parameters to 1, the note will
> dismiss too.
> It's true that I want to do a parallel simulation, but I
> don't which is the better way to solve this problem? Will the change
> of these parameters cause something wrong? Or is there anyting wrong
> with my .gro file?
> Thanks for your attention.
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
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