[gmx-users] Segmentation fault

Justin Lemkul jalemkul at vt.edu
Sun Aug 28 04:17:24 CEST 2016

On 8/27/16 5:32 PM, vivek naik wrote:
> I don't think you can do a simulation with pressure if you have position
> restraints, except if your restrained atoms are all in the same plane.

This is not true.

> However, ref_coordscaling option should be 'com', which should make it
> better than it is now.

"com" is just one possible option, but it is probably the most stable in most cases.

> Also, there is no way isotropic pressure is going to work. it has to be
> anisotropic (xy and z, with the first one being kept to zero).

Anisotropic means all box vectors can vary independently and is usually applied 
to crystals or other solid materials.  Coupling xy and z separately is 
semiisotropic and is usually used with membranes and surfaces.  For a simple 
aqueous protein system, isotropic is in fact correct.


> Vivek
> On Sat, Aug 27, 2016 at 12:15 PM, Seera Suryanarayana <palusoori at gmail.com>
> 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
>> PBC with trjconv command I got segmentaion fault error. I request you to
>> tell me What I did wrong and how to resolve it?
>> Thanks in advance
>> Surya
>> Graduate student
>> India.
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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 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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