On Fri, Mar 18, 2011 at 1:36 PM, Jason Swails <jason.swails.gmail.com>wrote:
> The restart is actually a full time step ahead with the coordinates (and a
> half time step ahead for velocities), I believe, so the last mdcrd frame
> won't match the ending restart file (but they'll be very close).
>
> ok. What I observed is the two structures are very different.
> Furthermore, if you're using the topology file to visualize your system,
> then you should not get any extra bonds that are not defined in that
> topology file. Perhaps your mdcrd file is corrupted? If you just use
> ptraj
> to dump the last frame as a PDB file, then VMD may be adding a bond between
> two atoms that are close to one another that won't be in the topology file.
>
> I load topology file first (AMBER7 PARM). then load mdcrd file (AMBER
COORDINATES).
I can play the movie to see everything is moving. but many bonds between
no-related atoms appear. How do you tell if the mdcrd file is not right?
Try loading frames into the topology file if you're not using that approach
> already.
>
> Good luck,
> Jason
>
> On Fri, Mar 18, 2011 at 10:07 AM, Bingwu Yu <amber.qna.gmail.com> wrote:
>
> > I did a short MD simulation. Then I use VMD to compare structure from rst
> > file to output crd file. they are not the same. I assume the structure
> from
> > rst file is the last frame of simulation.
> > The structure from output crd file looks strange too. bond shows up
> between
> > two non-related atoms . any idea?
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Fri Mar 18 2011 - 11:30:03 PDT
