From: Axel Kohlmeyer (
Date: Wed Aug 28 2013 - 04:52:20 CDT

On Wed, Aug 28, 2013 at 10:43 AM, Hamed Mortazavi
<> wrote:
> Hi,
> to visualize my polymer molecule I run a patch on VMD to create bonds
> between beads. this works well, but if I save the state and load it from
> .vmd file not only successive beads in polymer but all are shown bonded
> together. is this a mistake in patch or settings in VMD?

if you save the state in VMD you save the "visualization state", you
do *not* save the structure or coordinates. if you load the state back
into VMD, it will try to re-read the original coordinate files. if you
change the structure/topology and/or coordinates, you have to save
those as well to the corresponding files (or rather make copies of the
originals and then save).


> Best,
> Hamed.

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.