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 <depla...@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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists