[gmx-users] Re: why it is so slow

[Justin Lemkul]

On 11/2/12 12:23 PM, Albert wrote:
> Hello Vitaly:
>
> thanks a lot for kind comments.
> Do you have any idea why the running is so slow? Especially considering it is
> with GBSA model and my protein is only with 240 aa.
>

That system is not small, it's rather large.  Are you sure each replica is 
really running on 24 processors?  It occurred to me that there was a problem in 
4.5.4 that was fixed for 4.5.5, but the "fix" was really just a workaround, 
allowing a maximum of 2 processors if GBSA calculations were invoked in parallel:

http://redmine.gromacs.org/issues/777

Your log file will tell you for sure.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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