I try to remove the periodicity to get a new .xtc file and one .gro file. The commands are shown below: "trjconv -f original.xtc -s original.tpr -n index -o frame_0.gro -dump 0 -pbc nojump"
"trjconv -f original.xtc -s original.tpr -n index -o new.xtc -pbc nojump" When I use g_rms to calculate the rmsd by new .xtc and .gro file, there is a warning and other things goes well. Command i used is "g_rms -f new.xtc -s frame_0.gro -o rmsd.xvg" and the warning is "can not make broken molecules whole without a run input file,don't worry, mdrun doesn't write broken molecules". I think i have removed the boundary, and why it says there is an broken protein? Thanks. Jiaowei Tang On Thu, 2007-10-04 at 10:16 +0200, Tsjerk Wassenaar wrote: > Hi Jaowei Tang, > > Better use a .pdb or .gro file. Maybe the starting structure (obtained > after running pdb2gmx)? > By the way, if you removed the jumps over the boundary (you don't > really want to remove periodicity :p) you must already have a proper > structure. Or you can then extract the first frame from the trajectory > and use that as the starting point. > > Tsjerk > > On 10/4/07, tangxuan <[EMAIL PROTECTED]> wrote: > Dear all, > I am try to use g_rms to a protein, but its start structure in > the > simulation is not in one box. I removed the periodicity for > the xtc file > by trjconv, but do not know how to remove the periodicity in > the tpr > file. Could you give me some suggestions? > > Thank you. > > Jiaowei Tang > > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > -- > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php