[gmx-users] Regarding RMSD analysis result
ahmedo047 at gmail.com
Tue Sep 25 14:07:00 CEST 2012
trjconv -s top.tpr -f traj.xtc -o traj-nojump.xtc -pbc nojump
I hope it helps
2012/9/25 Archana Sonawani <ask.archana at gmail.com>
> 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.pinedadecastro at 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
> >> 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
> > out visually how the weird frames look like?
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> gmx-users mailing list gmx-users at gromacs.org
> * 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users