From: Axel Kohlmeyer (
Date: Sat Jun 06 2015 - 15:51:20 CDT

On Jun 6, 2015 10:05 PM, "Eric Smoll" <> wrote:
> Hello Axel,
> Thank you for the weekend reply. Thank you for recommending
the "mol bondsrecalc" command.
> 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,

Bond information can be accessed from the script interface. Either
directly, or through the topotools plugin.

> 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.
> Best,
> Eric
> On Sat, Jun 6, 2015 at 12:28 PM, Axel Kohlmeyer <>
>> 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
>> > connectivity from the structure file and this connectivity is not
>> > 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
>> > molecules. Is there a way to do this in VMD? Is there any other tool
>> > 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
>> > 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.