Hi Nahren, > trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc > trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter > tric -o center.xtc > trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc
> 1. The above procedures does not center the molecule in the box. You first center and then do a fit. The fitted trajectory will only be centered if the reference (proem.tpr) is (and then you can skip the second step anyway). > 2. The box seems to shift from one corner to the center. Especially for the > duration 8-12 ns (my restart run) What do you mean with this? Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
