[gmx-users] Limit mdrun runtime

Jack Shultz js at drugdiscoveryathome.com
Mon Sep 14 16:53:50 CEST 2009

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.


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