[gmx-users] Segmentation fault

vivek naik vivek.adishankara at gmail.com
Sat Aug 27 23:32:37 CEST 2016

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

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).


On Sat, Aug 27, 2016 at 12:15 PM, Seera Suryanarayana <palusoori at gmail.com>

> 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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Vivek Naik.

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