[gmx-users] Limit mdrun runtime

[Berk Hess]

If mdrun hangs -maxh won't help.
You can kill mdrun using the kill command.
But since mdrun catches signals, you might need kill -9 (the 'KILL' signal).

Berk

> Date: Mon, 14 Sep 2009 10:56:43 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Limit mdrun runtime
> 
> 
> 
> 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
> 
> -Justin
> 
> > -- 
> > 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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