[gmx-users] Segmentation fault mdrun

Alex s as1783 at hotmail.com
Sun Aug 31 19:52:47 CEST 2014

Thanks for the reply
I've attached a copy of my mdp file. It is a coarse grained system so a time step of 0.04 shouldn't be a problem. Regarding the link you've given, points 1 and 4 are not applicable to my situation, I've tried point 2 and found issues. What should I be looking for in point 3?
> Date: Sun, 31 Aug 2014 13:20:31 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Segmentation fault mdrun
> On 8/31/14, 1:17 PM, Alex s wrote:
> > Hi
> > I'd really appreciate some advice on this issue, I tend to get a segmentation fault during my mdrun. I've searched online for ways to resolve this and tried to diagnose whats causing this problem but I'm having no luck.
> > I know that if you get a segmentation fault at step 0 its most likely a problem with system configuration or a minimization issue. However for my system I successfully run energy minimization and equilibration. When I run md the segmentation fault occurs usually very late on the system (past the 100ns mark).
> > I've found that minor adjustments to the system can either lead to the error or remove it. For example for one system, I ran it ION free and I had no issues, however when I just replace 12 water molecules with NA+ and CL- this leads to a segmentation fault. Also I was able to fix this error in another system just by changing the time step from to 0.04 to 0.03.
> >  From what I'm describing, does it seem as if the fault lies with the system set up? or the mdp file? or could it be a compiler issue? What information should I be looking for in my output file to perhaps determine where issue lays?
> Provide the full .mdp file and people can comment on it.  Is this an atomistic 
> system?  A time step of 0.04 is insane if it is.
> Diagnostics: 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
> -Justin
> -- 
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
> http://mackerell.umaryland.edu/~jalemkul
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