From: Axel Kohlmeyer (
Date: Mon Sep 19 2016 - 09:47:15 CDT

On Mon, Sep 19, 2016 at 9:00 AM, Christian Wohlschlager
<> wrote:
> Dear ALL !
> I made a reaktion simulation with the following steps:
> the reaktion consist of 4 steps
> 1. first.pdb ---- dcd file with 100 frames
> 2. sec.pdb --- dcd file with 100 frames
> 3. tri.pdb ---- dcd file with 100 frames
> 4. four.pdb ---- dcd file with 100 frames
> then i copy first.dcd + sec.dcd + tri.dcd + four.dcd to all.dcd
> now i start first.pdb with all.dcd
> the bound which was createt between sec.pdb and tri.pdb is lost now
> when i start it sec.pdb with sec.dcd it ok
> i think there is something wronge that I DID in copy all together.

dcd files have no information about bonds, only coordinates.

in general, VMD assumes that you have the the same bond topology for
your entire simulation, so it will store the bond topology only for
the first frame and apply it to the remaining trajectory.
to visualize different bonding patterns, you have to take special care
and need to use a "dynamic bond" representation or use some dynamic
Tcl script processing that replaces/changes the bond topology during
the visualization or store each frame in a separate "molecule" and
then animate your trajectory by showing/hiding those individual
"molecules" instead of showing individual frames (-> multi-mol
animation plugin).


> Anybody knows or have any idea
> christian

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.