[gmx-users] Re: slow speed

Carsten Kutzner 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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100418/f0a3f664/attachment.html>

More information about the gromacs.org_gmx-users mailing list