I tried to visualize it on VMD and the molecule disappeared during these
frames
*Best Regards,
Esam
*
On Sun, Dec 18, 2011 at 3:27 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> If your system is periodic then it's possible this is from an imaging
> issue. If that is the case you could center on your solute and
> re-image. Have you tried visualizing those frames of the trajectory to
> see what is happening?
>
> -Dan
>
> On Sat, Dec 17, 2011 at 4:40 PM, Esam Tolba <eatolba.gmail.com> wrote:
> > I ran a simulation and from it I calculated RMSD. And all the values of
> > RMSD is flactuated from 0.9 to 2 but in fiive frames in the middle of the
> > simulation the value of RMSD jumped to 17. does anybody know what could
> be
> > the reason of that?
> > *Best *
> > *Esam*
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Postdoctoral Associate
> BioMaPS Institute, Rutgers University
> 610 Taylor Road
> Piscataway, NJ 08854
>
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Received on Sun Dec 18 2011 - 09:00:03 PST
