VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sat Aug 19 2017 - 01:27:26 CDT

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" <mailmd2011_at_gmail.com> 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
>
>