[gmx-users] removing pbc jumps from trajectory
x.periole at rug.nl
Mon Feb 21 09:01:54 CET 2011
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)
On Feb 21, 2011, at 8:52, Evelyne Deplazes <deplae01 at student.uwa.edu.au> wrote:
> 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"
> Evelyne Deplazes
> PhD student
> Theoretical Chemistry group
> University of Western Australia
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