[gmx-users] removing pbc jumps from trajectory

Evelyne Deplazes deplae01 at student.uwa.edu.au
Mon Feb 21 08:52:38 CET 2011


I have a series of trajectories from a coarse grained simulation (Martini
force field) that I ran using gromacs 4.0.4. The system consists of a
protein embedded in a POPC bilayer solvated with water. During the
simulation the protein (most of time its actually *part* of the protein)
jumps across the pb into the neighboring box. I use a series of tcl scripts
to analyse my trajectories and for that purpose I need to remove that
"period boundary jump" and make the protein "whole" again.

I have tried the approach described on the gromacs website

I also other combinations of -whole, -center and -pbc nojump of trjconv,
without any luck. Can anyone suggest how I can re-center the protein and
remove the pb jump ie make the protein "whole"


Evelyne Deplazes

PhD student
Theoretical Chemistry group
University of Western Australia
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