[gmx-users] GROMACS vs. AMBER speed comparison?
Mark.Abraham at anu.edu.au
Tue Aug 14 14:46:05 CEST 2007
Tsjerk Wassenaar wrote:
> 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.
JCTC December 2005, IIRC :-)
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