Hi, Yanmei On Fri, May 8, 2009 at 2:20 AM, Yanmei Song <yson...@asu.edu> wrote:
> NOTE 2 [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 > about note 2, the info given says if you run mdrun in parallel machine you may better make PME mesh load to below 0.5 to get optimal performace. If you run it just in a one-node machine, you may just ignore the note. But if in the first case of running in parallel, you can increase fft grid spacing a little (just try several values little larger)to lower PME mesh load to better distribute the computation among nodes. Regards, Yinhe Zhang
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