[gmx-users] Re: slow speed
ckutzne at gwdg.de
Sun Apr 18 12:56:14 CEST 2010
On Apr 16, 2010, at 1:40 AM, Shuangxing Dai wrote:
> I am not running in parallel. Right now I just changed links order from 12 to 4. It is still slow. While I change to shift, not Ewald, it finished 10000 steps in 10 mins. In the paper:
> J Comput Chem. 2005 Dec;26(16):1701-18.
> GROMACS: fast, flexible, and free.
> Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ.
> The performance there is around 10000 ps/day. I do not understand why my speed is so slow and it seems
> that Ewald option makes it slow.
why don't you use PME then? It can also be used in parallel.
Ewald is not optimized for speed.
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