[gmx-users] Segmentation fault mdrun

[Alex s]

They're ions that I've just added to the water phase of the system. That was a case I highlighted to show how sensitive the system is to minor changes. I have other systems which are ion free and still experience segmentation fault. 
I've just reviewed all my md runs for my systems, I have found that 2 of the systems which experienced segmentation fault had a warning that the pressure scaling was more than 1 %  . However the other systems that experienced segmentation fault presented no such warning yet the force imbalance was as high as 6 %. Could this be the issue? 
Thanks
Alex 

> Date: Sun, 31 Aug 2014 17:14:48 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Segmentation fault mdrun
> 
> 
> 
> 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
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> >   		 	   		
> >
> 
> -- 
> ==================================================
> 
> 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
> 
> ==================================================
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.