[gmx-users] GROMACS vs NAMD
ichorny at gmail.com
Tue Mar 4 16:24:38 CET 2008
>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
On Mon, Mar 3, 2008 at 11:33 PM, David van der Spoel <spoel at xray.bmc.uu.se>
> Dibyadeep Paul wrote:
> > Hii...
> > Could somebody kindly point out to me the essential difference between
> > the simulation procedures between NAMD and GROMACS. I am familiar with
> > NAMD, but since I am running it on a single processor machine I hear
> > that GROMACS would be much more efficient. Is there any comparison of
> > the results available on publicly available literature. If so it would
> > be very kind if somebody knowledgeable could kindly point that out to
> > me, or send me the relevent paper.
> On the GROMACS website there is a list of papers, one "neutral" paper
> did exactly this comparison, although it seems like they want to stay
> friends with everyone :). In the GROMACS 4 paper there is a comparison
> done by us with NAMD and Desmond figures from the literature. NAMD is
> roughly 4 times slower than GROMACS, predominantly because of single
> processor performance. However GROMACS 4 can also do constraints in
> parallel which means one can take larger time steps than with other
> packages, and this makes the gap even wider.
> > Sincerely
> > Dibyadeep
> > ------------------------------------------------------------------------
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> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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Ilya Chorny Ph.D.
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