Here are the steps that I used: 1. trjconv -pbc whole -dump 37.875 2. trjconv -pbc nojump 3. trjconv -center 4. g_select to make an index containing the atoms of interest 5. trjconv to extract coordinates
Regardless of whether step 1 is used or not, the resulting coordination shell configuration is not complete in the sense that it looks like the figure I posted previously. In all steps, I used the same .tpr file...is it possible that I need to generate a new one after step 1? Thanks, Blake PhD candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160p5012172.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
