[gmx-users] removing pbc jumps from trajectory

[XAvier Periole]

You have to make sure of two things:

1- use a reference (gro or tpr) where the molecule is whole! The tpr is prefered since the molecules are defined. 

2- with such a reference and the option -mol you'll get a trajectory with the protein as a whole. 

On that trajectory you may apply more modifications: 
-nojump with generate a trajectory where the pbc are not applied so you can do msd analysis. Note that thisnis done by default in g_msd. 
- fitting with only translation removed (equivalent to centering but more stable. Centering works strangely)

XAvier.  

On Feb 21, 2011, at 8:52, Evelyne Deplazes <deplae01 at student.uwa.edu.au> wrote:

> Hi 
> 
> 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 http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> 
> 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"
> 
> Thanks 
> Evelyne 
> 
> -- 
> Evelyne Deplazes
> 
> PhD student 
> Theoretical Chemistry group
> University of Western Australia 
> 
> -- 
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