Hi Leila, Maybe you're better off trying:
1. trjconv -pbc nojump # choose system for output 2. trjconv -center -pbc mol # choose protein/dna for centering, system for output Centering is done before removing PBC, so you should be safe with two passes. You might also want to play with -ur to get the best looking representation. Just try some things and see what it does :) Hope it helps, Tsjerk On Wed, Oct 27, 2010 at 10:05 AM, leila karami <karami.lei...@gmail.com> wrote: > Hi Carsten > > > > Thanks for your answer. You got my case very well. > > > > I understand your mean as follows: > > 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water) > > 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group > =protein-dna) > > Is that true? > > You said, (Then overlay both results in the visualization program). How? > > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
