On Sun, Dec 18, 2011 at 11:42 AM, Esam Tolba <eatolba.gmail.com> wrote:
> I tried to visualize it on VMD and the molecule disappeared during these
> frames
>
Molecules don't "disappear" in VMD. It may have jumped into an area that
wasn't in the visible scope, but they didn't "vanish". Try changing the
representation of those atoms to VDW (to make them much larger), then zoom
out until you see them.
*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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> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Postdoctoral Associate
> > BioMaPS Institute, Rutgers University
> > 610 Taylor Road
> > Piscataway, NJ 08854
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Dec 19 2011 - 08:30:07 PST
