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
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