On 26/01/2011 12:05 AM, Justin A. Lemkul wrote:
gromacs wrote:
HI Friends,
I get the following note,
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale
thermostat.
I want to keep the T at 300K, so does it matter to select any
thermostat method?
The choice of thermostat certainly does matter, otherwise you wouldn't
get this note. Refer to the numerous discussions in the list archive
as to why one would or would not (usually) use the Berendsen
thermostat, as well as:
http://www.gromacs.org/Documentation/Terminology/Thermostats
http://www.gromacs.org/Documentation/Terminology/Berendsen
... and the relevant manual sections.
Mark
Another note when i use PME:
Estimate for the relative computational load of the PME mesh part: 0.97
NOTE 1 [file aminoacids.dat, line 1]:
The optimal PME mesh load for parallel simulations 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
So what is the reason? I use type=PME
Your combination of settings (rcoulomb, fourierspacing, and perhaps a
few others) indicate that your simulation is going to spend an
inordinate amount of time doing PME calculations, so your performance
will suffer. Seeing your entire .mdp file would be necessary if you
want further guidance.
-Justin
Is my setting proper?
Thanks
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