Hello Justin My problem is fixed I am very grateful for your help.
I used from bellow commands: * * *1- make_ndx -f md.tpr * * >r 1-16 ----->DNA have 32 residue 2- trjconv -s md.tpr -f wi_md.xtc -n index.ndx -o md.pdb -center -pbc mol * * 2-1- for centering ---> residue 1-16 ---> new group * * 2-2- for pbc ----> DNA ----> group 1* You have been a big help to me. So Thanks -- 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
