[gmx-users] Segmentation fault mdrun

[Justin Lemkul]

On 8/31/14, 1:55 PM, Alex s wrote:
>
> There was a typo in the last message, I found NO issues in point 2.

Actually, you did.  You said when you removed the ions, the problem was 
resolved.  That indicates to me that the ions are somehow unstable.  I don't 
know much about doing CG simulations, so maybe someone else can advise, but it 
seems that the long time step is causing large forces to accumulate on the ions 
and you get the crash.  Are the ion particles just a single ion or some 
representation of a hydrated ion?

-Justin

> From: as1783 at hotmail.com
> To: gmx-users at gromacs.org
> Date: Sun, 31 Aug 2014 18:52:39 +0100
> Subject: Re: [gmx-users] Segmentation fault mdrun
>
> 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?
> Thanks
> Alex
>> 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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>   		 	   		
>

-- 
==================================================

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

==================================================