VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 30 2017 - 17:49:12 CDT

On Fri, Jun 30, 2017 at 6:11 PM, MD Simulation
<mdsimulationgroup_at_gmail.com> wrote:
> Hello,
>
> Are there any trajectory formats that VMD can read that allows for dynamic
> bond breaking and forming that would adjust fragment count during
> visualization? Basically an auto- mol reanalyze, mol bondsrecal.

no. it is not a file format issue, but an issue of the molfile reader
API and how bond information is stored in VMD.
the fundamental assumption is, that bonds don't change (because they
don't in regular classical MD).

however, you can define a procedure that calls mol bondsrecalc and
then mol reanalyze and hook it via a variable trace into the animation
loop.

axel.

>
> Thanks 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.