[gmx-users] Segmentation fault

Seera Suryanarayana palusoori at gmail.com
Sat Aug 27 08:53:06 CEST 2016

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
Graduate student

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