[gmx-users] Limit mdrun runtime

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 14 16:56:43 CEST 2009

Jack Shultz wrote:
> Hello,
> I have developed a workflow for prepping structures. One problem I have 
> is sometimes it gets hung up on mdrun. Are there any mdrun parameters we 
> can use to kill this process if it runs too long?  The parameters we are 
> using should not run over 5 minutes. I have not figured out how to do 
> this with my script, but I guess there may be a way using SIGALRM.

mdrun -maxh


> -- 
> Jack
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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