Hi Mark,<br>Thanks for your quick response.<br><br><div class="gmail_quote">2009/10/8 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">vivek sharma wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi There,<br>
While running a parallel MD simulation, I got following message while playing with parameters:<br>
NOTE 3 [file aminoacids.dat, line 1]:<br>
The optimal PME mesh load for parallel simulations is below 0.5<br>
and for highly parallel simulations between 0.25 and 0.33,<br>
for higher performance, increase the cut-off and the PME grid spacing<br>
---------------------------<br>
<br>
I don't have any idea when a run should be called a highly parallel simulation?<br>
</blockquote>
<br></div>
Well below 224 :-)<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Is it depend on problem-size or the number of processor we are using?<br>
</blockquote>
<br></div>
Processors.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I am trying to optimize my simulation to run on 224 processors and system consist of:<br>
<br>
Total atom count = 54640<br>
where water molecules = 17074<br>
</blockquote>
<br></div>
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.<div class="im">
<br></div></blockquote><div>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?<br>Is it the PME load or something else?<br>
<br>Thanks,<br>Vivek<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Also, I am getting following message while running grompp<br>
---------------------------------<br>
NOTE 1 [file md.mdp, line unknown]:<br>
The Berendsen thermostat does not generate the correct kinetic energy<br>
distribution. You might want to consider using the V-rescale thermostat.<br>
------------------------------------<br>
Any insight in the above message will be highly appreciated.<br>
</blockquote>
<br></div>
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.<br>
<br>
Mark<br>
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</blockquote></div><br>