[gmx-users] Optimizing a parallel simulation

vivek sharma viveksharma.iitb at gmail.com
Thu Oct 8 08:20:39 CEST 2009

Hi Mark,
Thanks for your quick response.

2009/10/8 Mark Abraham <Mark.Abraham at anu.edu.au>

> vivek sharma wrote:
>> 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?
> Well below 224 :-)
>  Is it depend on problem-size or the number of processor we are using?
> Processors.
>  I am trying to optimize my simulation to run on 224 processors and system
>> consist of:
>> Total atom count = 54640
>> where water molecules = 17074
> You will want to tweak rcoulomb and fourier_space like the above message
> says. Even so, with less than 500 atoms per particle-particle processor you
> may find yourself spending more time communicating than processing. I
> suspect your system may be too small to get value from so many processors,
> even if you have good network (e.g. Infiniband). You will wish to read 3.17
> of the manual to start understand the issues involved here.
Thanks for pointing me to the rel;ated section in the manual. While tweaking
the rcoulomb and fourier_space values, what parameter need to be observed
for checking the result?
Is it the PME load or something else?


>  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.
> Seems self-explanatory to me - you're using Berendsen and that might not be
> the right choice. Read the manual sections about the different thermostats.
> Mark
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