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. Hi,
why don't you use PME then? It can also be used in parallel. Ewald is not optimized for speed. Carsten
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
