[gmx-users] Energy minimizations taking really, really long?

Justin Lemkul jalemkul at vt.edu
Wed Oct 23 13:54:35 CEST 2013

On 10/22/13 9:57 PM, Nimmy McNimmerson wrote:
> I have some simulations of inserting a probe molecule into a bilayer. Some molecules work fine. However, a certain class of molecules is taking an absurdly long time to run the exact same simulation, even though I energy minimized the molecules individually beforehand and there are no overlaps. What might be going wrong?

Please clarify - your subject line says the EM is taking a long time, but the 
content here suggests the post-EM simulation process is the problem.  Which is 
it?  Are you sure the .mdp files were identical?  Small changes can have big 
effects on performance.  Are you sure the hardware is fully functional?  A stuck 
node or lagging file system can explain "slow" runs.  If mdrun is still churning 
along without crashing, most likely the problem is external.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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