From: John Stone (
Date: Wed Jul 21 2010 - 13:08:34 CDT

  I assume that this "extra" line is a bond that's either crossing
a periodic boundary, or something similar. If you don't see it after
saving to a separate file and reloading, then this is likely because it
was determined by VMD automatically (PDB files don't contain explicit
bonding info for any but special cases), using a distance-based bond
determination heuristic. You can either ask VMD to recompute the bonds
and re-analyze the molecular structure using a simulation frame that doesn't
have this issue, or load a PSF or similar file that provides VMD with
full bond information, either way should cure the problem if it's just
an issue with distance-based bond determination. If on the other hand,
the issue is a periodic cell wrapping, then you may need to unrwap your
trajectory to prevent that from happening, in which case you would want
to use the "pbctools" plugins for that, which have been discussed on the
mailing list many times before, so a quick search through the archive or
a look at the docs should help you if that's the case.

  John Stone

On Wed, Jul 21, 2010 at 01:26:08PM -0400, Elias Ahadi wrote:
> Hello,
> I have a problem in displaying a simulation in VMD. My trajectory file is in PDB format and contains 2500 frames. My simulation consists of 1000 waters, 4 ions and a model protein chain. When I open my trajectory file, VMD seems to display an "extra line" between 2 water molecules that are on opposite sides of the water cluster. I display the waters as LINE and other constituents as VDW representations. This problem disappears if I display all the atoms in VDW format.
> The other odd thing is that if I extract 1 frame of my simulation and copy it to a blank PDB file and open that with VMD, it does not display the "extra line" between the 2 waters even in LINE format.
> Has anyone else out there come across this problem and if so is there a solution to this.
> Really appreciate if anyone has some ideas.
> Thanks,
> Elias

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