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: as1...@hotmail.com
To: gmx-us...@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: jalem...@vt.edu
To: gmx-us...@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
jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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