[gmx-users] Segmentation fault mdrun

[Justin Lemkul]

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

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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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