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

Justin Lemkul jalemkul at vt.edu
Fri Nov 2 17:48:24 CET 2012

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:


Your log file will tell you for sure.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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