Hi Mark, Thanks for your quick response. 2009/10/8 Mark Abraham <mark.abra...@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? Thanks, Vivek > > 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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