From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 08 2005 - 18:48:11 CDT

Bob,
  I haven't seen this type of problem before. VMD should be
preserving the same bonding pattern for all timesteps with the
one exception of if you have use the "DynamicBonds" representation,
which recalculates bonds on-the-fly with a distance based bond
search method. If you're getting bonds appearing and disappearing,
this may indicate a problem with the gromacs trajectory reader plugin
or some other issue that we haven't seen before. If you have a short trajectory
file that exhibits the problem, I'd be happy to take a look and see
what I can figure out. If you send me a URL to a web page containing
the trajectory and structure files that go with it, I'll download them
and give it a run here. One other useful bit of information I'll also
want to know is what platform you're running on, and which version of
VMD you're using.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 08, 2005 at 11:42:13AM -0400, Bob Johnson wrote:
>
> Hello,
> I am doing some simulations in GROMACS with carbon nanotubes. Initially VMD
> recognizes the C-C nearest neighbors and draws bonds between them. However,
> when I view the trajectory generated by GROMACS VMD no longer draws the bonds.
> In addition to a trajectory, GROMACS generates a restart file that contains the
> last frame of simulation. When I view this restart file in VMD, the bonds are
> drawn. Do es anyone know how to visualize the bonds throughout the whole
> trajectory and why VMD doesn't draw them in automatically?
> Thanks,
> Bob Johnson
> University of Pennsylvania

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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