From: Eric Smoll (
Date: Fri Jun 05 2015 - 22:31:53 CDT

Hello VMD users,

I am working with reactive QM/MM trajectories computed in GROMACS (.gro
structure file + .xtc trajectory file). VMD appears to compute the
displayed connectivity from the structure file and this connectivity is not
dynamic unless the "dynamics bonds" drawing method is used.

I am interested in computing kinematic properties of dynamically defined
molecules. Is there a way to do this in VMD? Is there any other tool that
might be capable of this?

I find that the "dynamics bonds" drawing method works well in most
situations but many of my trajectories evolve hydrogen gas from organics
and the H2 bond is never rendered over the H2 vibrational period. Is there
a reason this might be?