Hi, trjconv -s top.tpr -f traj.xtc -o traj-nojump.xtc -pbc nojump
I hope it helps 2012/9/25 Archana Sonawani <ask.arch...@gmail.com> > Hi, > > Your RMSD graph is ok but is represented wrong due to pbc problem. Use > whole and nojump options of trjconv. > > On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD < > luis.pinedadecas...@lnu.se> wrote: > > > On 09/25/2012 10:08 AM, naga sundar wrote: > > > >> Dear Felipe > >> > >> Thanks for ur reply. > >> > >> The system is a protein-protein complex. Like u r saying its > due > >> to pbc problem then why any abnormality doesn't happened to the native > >> complex (Black line)?. > >> > > Maybe because MD is stochastic ... > > > > > > As already suggest by justin i checked the pbc > >> conditions upto my knowledge everything is fine. > >> > > As Justin said, it's not about the pbc conditions as they appear in the > > mdp file, but about pbc effects due to a chain, probably the ligand, > > leaving the box and being reflected to the opposite side. Have you > checked > > out visually how the weird frames look like? > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > * Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > 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< > http://www.gromacs.org/Support/Mailing_Lists> > > > -- > 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 > -- Ahmet Yıldırım -- 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