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 :-)
Mark
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