Hi Evelyne, > 1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc
The option -pbc mol IIRC relates to the option for the unit cell representation (-ur). To unbreak molecules using trjconv, you need to have .tpr file and use the option -pbc whole. > 2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc > if I use 1) and 2) the system gets "ripped" apart. The system is no longer a > box but a flat disk (very funky) This is because the jumps are removed and over time the lipids diffuse in the plane. They've diffused quite a bit probably, smearing themselves out over a disk. Groetjes, Tsjerk -- 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
