[gmx-users] GROMACS & Speed

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 7 16:49:24 CET 2006

Omololu Akin-Ojo wrote:
> Hi,
> i use GROMACS & i like it because it is so fast. But, i would like to 
> know if GROMACS "cut corners" ? Otherwise, why is it is so fast?
> if you have a fortran compiler on an Opteron box, GROMACS does not use 
> the assembly loops. Right? So, why is it blazingly fast?
> o.

gromacs does not cut corners...
Most important we do not compute stuff that we know will give zero as a 
result anyway, this gives 20-30% compared to other codes.
Single precision is a factor of two faster than double, assembly is a 
factor of two faster than C/Fortran, and finally our innerloops are 
completely unrolled, this probably also gives a factor of 1.5.
So if you multiply it all you have a significant factor (even in double 

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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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