Hi Sara, The problem is that your micelle is formed at the end of the trajectory. To get what you want, you need to mirror the trajectory, follow the procedure you followed, and mirror the resulting trajectory. I posted a piece of python code for mirroring a trajectory a while back: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061443.html
Hope it helps, Tsjerk On Wed, Dec 28, 2011 at 5:25 PM, mohammad agha <mra...@yahoo.com> wrote: > Dear GROMACS users, > > I have a problem about trjconv -pbc nojump, I have 2 micelles in the end of > my simulation. For analysis I should do three steps for micelle clustering > at > http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering > Steps 1 and 2 work good and when I view my trajectory after step2 by : > ngmx -f a_cluster.gro -s a_cluster.tpr > is viewed 2 micelles, but when I did step 3 (trjconv -nojump) and after do : > ngmx -f a_cluster.xtc -s a_cluster.tpr > has been created 1 micelle and reminder of monomers have been collected as > some groups at different places. > May I ask you to help me, please? > Thank you > > Best Regards > Sara > > > > -- > 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
