<html><body bgcolor="#FFFFFF"><div><br></div><div>You have to make sure of two things:</div><div><br></div><div>1- use a reference (gro or tpr) where the molecule is whole! The tpr is prefered since the molecules are defined. </div><div><br></div><div>2- with such a reference and the option -mol you'll get a trajectory with the protein as a whole. </div><div><br></div><div>On that trajectory you may apply more modifications: </div><div>-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. </div><div>- fitting with only translation removed (equivalent to centering but more stable. Centering works strangely)</div><div><br></div><div>XAvier. </div><div><br>On Feb 21, 2011, at 8:52, Evelyne Deplazes <<a href="mailto:deplae01@student.uwa.edu.au">deplae01@student.uwa.edu.au</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div>Hi <br><br>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. <br>
<br>I have tried the approach described on the gromacs website <a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions"><a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a></a><br>
<br>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"<br><br>Thanks <br>
Evelyne <br><br>-- <br>Evelyne Deplazes<br><br>PhD student <br>Theoretical Chemistry group<br>University of Western Australia <br><br>
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