From: Axel Kohlmeyer (
Date: Mon Aug 15 2011 - 12:07:13 CDT

On Mon, Aug 15, 2011 at 12:09 PM, Moeed <> wrote:
> Hello all,
> I have a problem visualizing my structure in vmd. Once I load structure and
> trajectory files file I see some artificial bonds connecting all atoms while
> there is no bond between them. Has anyone any ideas why this is happening?

this is next to impossible to answer without knowing
what kind of data (format) you are using and exactly
what you are looking at.

overall, there are two issues that you have to keep
in mind.
1) VMD will automatically build a bond topology, if
   the file format that you use doesn't provide this info,
   e.g. a PDB file. these bonds are based on guesses,
   that may be very wrong for your system.
2) VMD doesn't allow the bond topology to change
   in a trajectory. so if the order of atoms changes
   over time and then you get weird bonds. the same
   can happen with atom positions wrapped back into
   the principal unit cell.


> Thank you,

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.