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
