[gmx-users] Segmentation fault

Justin Lemkul jalemkul at vt.edu
Sun Aug 28 04:15:30 CEST 2016

On 8/27/16 2:45 AM, Seera Suryanarayana wrote:
> Dear gromacs users,
> I have done mdrun for 10ns with position restrain of interest of our
> residues. Here I woulk like to explain how I did the position restrain.
> During gmx pdb2gmx command we usually get posre.itp file which we use in
> the equilibrium process to restraint the protein. As I want to do real
> mdrun with restraint on some residues, I just edited the posre.itp file and
> kept the restrain information only for residues of my interest and I define
> in the md.mdp file as "define  =_DPOSRES       ; position restrain the
> protein".  I haven't anything to the topology file. When I executed the
> grompp command I got following warning and then error.
> WARNING 1 [file md.mdp]:
> you are using pressure coupling with absolute positions restraints, this
> will give artifacts. use the refcoord_scaling option and the error was too
> many wanrings[1], gmx terminated. Then I executed grompp with the -maxwarn
> 1. After preprocessing  I did simuations for 10ns. When I try to remove the

Don't use -maxwarn.  Fix the problem.  You need some sort of reference 
coordinate scaling when applying position restraints in an NPT ensemble.

> PBC with trjconv command I got segmentaion fault error. I request you to
> tell me What I did wrong and how to resolve it?

What was the trjconv command?  What was the actual screen output?  Seg faults 
are usually bugs, but if you're doing something weird that you shouldn't be, it 
could be entirely unrelated to anything to do with the run itself.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list