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
--
========================================
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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