[gmx-users] GROMACS vs NAMD

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 4 08:33:16 CET 2008

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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