From: Vermaas, Joshua (
Date: Fri Jun 30 2017 - 18:04:29 CDT

No. Fragments and bonds are datastructures that VMD stores per molecule,
and if you want them to change at every frame, they would need to be
recalculated at every frame.

On 06/30/2017 05:00 PM, MD Simulation 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.
> Thanks