[gmx-users] Optimizing a parallel simulation

vivek sharma viveksharma.iitb at gmail.com
Thu Oct 8 07:54:14 CEST 2009

Hi There,
While running a parallel MD simulation, I got following message while
playing with parameters:
NOTE 3 [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

I don't have any idea when a run should be called a highly parallel
Is it depend on problem-size or the number of processor we are using?

I am trying to optimize my simulation to run on 224 processors and system
consist of:

Total atom count = 54640
where water molecules = 17074

Also, I am getting following message while running grompp
NOTE 1 [file md.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.
Any insight in the above message will be highly appreciated.

Please advice me how to optimize the parameters to run the simulation with
maximum efficiency.

With thanks in advance,
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