>From my own personal experience, I get better performance on 8 processors running gromacs 3.3.1 then I did with 32 processors running NAMD. Note my 8 processors are all on one motherboard and the 32 processors was across 4 machines. All GigE. Roughly 100K atoms. Also not this is all done on a Windows cluster.<br>
<br><br><div class="gmail_quote">On Mon, Mar 3, 2008 at 11:33 PM, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="Wj3C7c">Dibyadeep Paul wrote:<br>
> Hii...<br>
><br>
> Could somebody kindly point out to me the essential difference between<br>
> the simulation procedures between NAMD and GROMACS. I am familiar with<br>
> NAMD, but since I am running it on a single processor machine I hear<br>
> that GROMACS would be much more efficient. Is there any comparison of<br>
> the results available on publicly available literature. If so it would<br>
> be very kind if somebody knowledgeable could kindly point that out to<br>
> me, or send me the relevent paper.<br>
</div></div>On the GROMACS website there is a list of papers, one "neutral" paper<br>
did exactly this comparison, although it seems like they want to stay<br>
friends with everyone :). In the GROMACS 4 paper there is a comparison<br>
done by us with NAMD and Desmond figures from the literature. NAMD is<br>
roughly 4 times slower than GROMACS, predominantly because of single<br>
processor performance. However GROMACS 4 can also do constraints in<br>
parallel which means one can take larger time steps than with other<br>
packages, and this makes the gap even wider.<br>
><br>
> Sincerely<br>
><br>
> Dibyadeep<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
<div class="Ih2E3d">><br>
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<br>
</div><font color="#888888">--<br>
David van der Spoel, Ph.D.<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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