From: Axel Kohlmeyer (
Date: Sun Mar 09 2014 - 03:37:28 CDT

On Sun, Mar 9, 2014 at 7:52 AM, T K <> wrote:
> Dear VMD mailing list
> I am pretty new to using VMD so excuse me if this questions is a silly one.
> I have a simulation with a changing number of bonds which I want to
> visualize but cannot do so with DynamicBonds.

why not?

> My simulation is run on lammps
> so what i tried to do is simple write a datafile withe write_data and then
> loop over all the data files load them and create an imagefile, afterwards
> to animate them using an external program. But I am guessing there is a much
> easier way to do it completely in VMD ?

depends. in general, VMD assumes that your bonds don't change. if they
do, you have to use some tricks. those tricks usually require some
tinkering and often some scripting, and not everything will work
exactly as if your bonds would not change.

you can also do the same kind of visualization from inside LAMMPS
using the dump image command and automagically create an animation
using dump movie. that is assuming that you do have bond information
present, of course.

> Hope you can help me, thank you !
> Taj

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