From: Axel Kohlmeyer (
Date: Tue Aug 28 2007 - 12:05:46 CDT

On Tue, 28 Aug 2007, Eduard Schreiner wrote:

ES> Dear all,
ES> I have a small question concerning the selection keyword "numbonds".
ES> To me it looks that "numbonds" is not updated during a trajectory, rather it appears that
ES> the number of bonds is calculated once (for the first frame) and is used for all
ES> following ones in the trajectory.
ES> Is this behaviour intended?

hi eddi,

yes. this is the way it is currently supposed to work.

the bonds are traditionally defined in the topology
file and (in classical MD) don't chance over the course of
a simulation. this is back drop that VMD was developed on.
for people using VMD on ab initio MD this may be inconvenient.

however you can do:

mol bondsrecalc <molid>

to force VMD to recalculate the bond information from its
default heuristics for the current timestep. for that to
work well, you should make sure that all atoms have proper
'radius' values.


ES> eddi

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.