[gmx-users] GROMACS vs. AMBER speed comparison?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Aug 14 09:02:48 CEST 2007

Hi Seungpyo Hong,

> Hi, gmx-users,
> Recently I have try to use AMBER 9 for the simulation of protein with about
> 300 residues.
> Surprisingly, I found that AMBER is far slower than GROMACS; GROMACS is
> about twice faster.
> I can not figure out the reason.
> Why is GROMACS faster than AMBER?
> Could anybody know the reason?

The reason is that the developers wanted it to be faster and put time
in thinking about the routines. The actual cause of the differences in
speed are well described in the special issue of JCC, december 2005 on
MD packages, and on the web site, as suggested by Yang Ye.



> Or have I made a mistake in AMBER or GROMACS simulation?
> If anybody has compared the speed of AMBER and GROMACS, please tell me the
> result.
> Thank you~
> --
> --------------------------------------------------
> 'God used beautiful mathematics in creating the world.'
> -Paul Dirac
> 'But he created too many object.'
> -Seungpyo Hong
> Seungpyo Hong
> Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
> Tel. (82)-18-372-2468
> sphong_ at kaist.ac.kr
> sp1020 at gmail.com
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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