From: Jeffrey Potoff (
Date: Tue May 01 2012 - 19:53:12 CDT

On 5/1/2012 5:14 PM, gökçe ayşe güven wrote:
> Hi all,
> I have 400ns simulation for 1mrp protein system and after 140ns half
> of my protein system moves out of the PBC cell, for that reason, -for
> specific frames- distance between 2 selected atoms (Fe iron and Glu
> residue CA atom) jumps 60 angstrom in 2ps which is impossible. In
> short, I want to keep my protein at the center of my PBC cell for all
> frames. I tried moveby, pbctools, etc. but they didn't work. Could
> anybody help me please?
> --
> Gökçe Ayşe Güven

It is (also) relatively easy to solve this problem using the GROMACS
trajectory manipulation tool trjconv

Jeffrey J. Potoff
Associate Professor			  Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815