From: John Stone (
Date: Mon May 02 2005 - 09:54:50 CDT

  Does VMD crash on your machine if you run it in text mode, or only
when in graphics mode? Try loading the troublesome structure in text
  vmd -dispdev text
  mol new crashme.pdb

Mail me a copy of the PDB file(s) that give you problems and I'll take a look.

  John Stone

On Mon, May 02, 2005 at 05:38:25PM +0800, Stefano Piana wrote:
> Hi all,
> I have been using VMD for a long time without any problem. Now I
> installed VMD on a new machine running RHEL 3 and VMD (both 1.8.2 and
> 1.8.3) crashes while loading PDB files. I tried to track the bug and I
> found out that the crash occurs when the number of bonds in a file
> exceed a certain number (about 1000). If I turn all the atoms to
> hydrogen in the PDB file I can easily load and display a PDB file
> containing 1M atoms in VDW representation, therefore it looks to me that
> there is no problem with the graphic libraries. As soon as I have heavy
> atoms around VMD immediately crashes if the file I try to load contains
> more than a few hundreds atoms.
> Just to rule out any problem with the PDB format I have tried with PDB
> files coming from all sort of sources (gromacs, the protein data bank,
> the examples coming with VMD).
> Any suggestion?
> Stefano

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