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).
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.
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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Received on Fri Mar 18 2011 - 11:00:03 PDT
