Hi Gloria,
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:
www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/index.html
Carsten
On Aug 31, 2009, at 1:51 PM, 秦光荣 wrote:
hello:
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.
Gloria
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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
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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