[gmx-users] Regarding RMSD analysis result

[ahmet yıldırım]

Hi,

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>

> 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.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
> 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?
> >
> >
> > --
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