Sorry forgot to add::: by doing this I can see my polymer near the center of box
On Mon, May 6, 2013 at 11:21 AM, gromacs query <gromacsqu...@gmail.com>wrote: > Dear All, > > I want to calculate water and ions density around polymer. After MD I see > my polymer goes near the edges of box and rather some part is out of box. > So in order to calculate water and ion density I think polymer should be > near the center of box (please correct me if wrong) > > So by doing this: > > trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc > mol -center > > Select group for centering: I selected my polymer only > Select group for output: I selected all atoms (polymer + water + ions) > > Please let me know is this correct way of modifying trajectory to > calculate water and ion density? > > regards, > Jiom > -- 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
