From: Axel Kohlmeyer (
Date: Fri Jul 16 2010 - 12:47:26 CDT

On Fri, Jul 16, 2010 at 12:54 PM, Edward Lyman <> wrote:
> Hi all,

hi ed,

> I have a trajectory, but it is not a trajectory of a molecular system.
> Rather it is a trajectory of a bunch of points in a plane that are
> projections of the SASA of a molecular system. I have them stored in xyz
> format, but each frame in my trajectory naturally has a different number of
> points. Also, when I attempt to naively load the entire trajectory into vmd,
> it fails on the second frame with lots of errors about too manty bonds, as
> it tries to connect this points into a molecule.

this can be turned off when using autobonds 0 in combination with
mol new.

> Is there a simple way to load a stack of, say, 200 snapshots of my points
> and then stack them into an animation? All the scripts I see on the website
> seem to work only for a trajectory that has the same number of points in
> each frame.

the fact that VMD expects the same number of atoms in each frame is
deeply engraved into the VMD source and thus this restriction is not
easily lifted.

there are currently two workarounds:

1) split your trajectory into individual frames, load each into a
separate molecule
    and use the multimolanim plugin to show only one of them at a time.

2) pad each frame with dummy atoms that can be made invisible.
    for the latter, i have written a script that is part of v1.1 of
the topotools plugin.
    topo readvarxyz will read the file and then you can show
    only the atoms in the current frame with a selection of "user > 0.5"
    instead of "all".

let me know if you need help with any of the two.


> Thx,
> Ed

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.