From: Eric Smoll (
Date: Sat Jun 06 2015 - 14:55:07 CDT

Hello Axel,

Thank you for the weekend reply. Thank you for recommending the "mol

I assume that adding another pass to the bond detection scheme requires
editing the source, correct?
Is there a way to access the bonding data reported by bondsrecalc? If so, I
could correct for the presence of hydrogen after pulling data from
bondsrecalc. I am less interested in visualization and more interested in
processing trajectory data.


On Sat, Jun 6, 2015 at 12:28 PM, Axel Kohlmeyer <> wrote:

> On Sat, Jun 6, 2015 at 5:31 AM, Eric Smoll <> wrote:
> > 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.
> correct. for performance and storage efficiency reasons VMD assumes
> trajectories are from a classical MD simulation without changes.
> > 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?
> that depends on what kind of heuristics you want to use to determine
> the bonding topology. the heuristics in VMD are fairly simple. it is
> based on the atomic radii that VMD guesses from the names of the atoms
> (unless you provide diameter information to overwrite it) with the
> additional restriction to not have bonds between two atoms that are
> detected as hydrogens. that gets a decent result for most people that
> use VMD. if that is sufficient for you, you can trigger a recomputing
> of the bond topology from the script interface through the "mol
> bondsrecalc" command.
> > 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?
> yes. the simple distance based heuristic would determine a lot of
> unphysical H-H bonds where both H atoms would be connected to another
> atom. H2 molecule bonds could only be reliably detected by adding
> another pass to the bond detection scheme.
> axel.
> >
> > Best,
> > Eric
> --
> Dr. Axel Kohlmeyer
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.