From: Jana, Suvamay (
Date: Sat Aug 19 2017 - 04:00:40 CDT

Try with dynamic bond option in vmd which you can find in the drawing
method. Hope that may help.

Suvamay Jana
Grad student
Dept of Chemical and Materials Engineering
University of Kentucky

On Fri, Aug 18, 2017 at 11:27 PM, Ashar Malik <> wrote:

> I might be wrong about this, but I think at present it may not be possible
> directly.
> In case of a charmm based simulation ... To visualize the binary
> trajectory you pre load a structure file (psf) which then remains identical
> for all subsequent frames in the trajectory. This is relevant because the
> psf holds the information on bonds e.g. if atom A and atom B have a bond
> there is no reason for that bond to be updated. (classical MD doesn't
> support bond breaking) .... So like I said I might be wrong but I don't
> think there exists a way to update the psf. Without updating the psf you
> can't tell VMD that the bonds have formed in a new way.
> when the bonds break or form in a new way you would need the topology for
> the new Residue that may form as a result of changes in bonds to update the
> psf. This seems like the longer way. Another that I can think of is that
> given bonds are distance based you can have a pairwise matrix of distances
> which writes out new connectivity Everytime a pairwise values crosses a
> threshold.
> These are just some thoughts ... they may or may not work. Perhaps you can
> wait and you might get a better reply from someone better informed on
> loading trajectories from hybrid methods.
> On Aug 19, 2017 5:45 PM, "Albert" <> wrote:
>> Hello,
>> I have finished a QM/MM calculation and imported the trajectory into VMD.
>> I played the movie in VMD and found that the bonds were not updated
>> according to QM/MM calculation. Some bond is distorted to unusual long
>> instead of forming a new bond with new atoms.
>> So I am just wondering how shall we tell VMD update bond connections
>> according to atom distance automatically for playing trajectory?
>> thanks a lot
>> Alberrt

With Regards,
Suvamay Jana