[gmx-users] Optimizing a parallel simulation

[vivek sharma]

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
simulation?
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,
Vivek
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091008/9e2921e3/attachment.html>