From: Norman Geist (
Date: Mon Dec 09 2013 - 08:58:33 CST

You can do that easily with a script, looping over the frames, if you know
about tcl. To find out how to change the transparency of a material, try VMD
Main->File->Log Tcl Commands to Console. Afterwards you can do by hand what
you want to change using the gui, and check the console for the particular
commands. You could set a start and end opacity. The difference devided by
number of frames or "frames/framesperfade" is your step then. The command
you need would look like

material change opacity Transparent 0.34

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Gaetano Calabró
> Gesendet: Montag, 9. Dezember 2013 12:55
> An:
> Betreff: vmd-l: Change transparency along a trajectory
> Hi there,
> I would like to change the transparency of a set of atoms along a given
> trajectory. For example at beginning of the trajectory the atoms are
> full opaque but at the end they are full transparent and in between the
> transparency should linearly change. How can I dot it scripting or
> using the VMD GUI?
> Thanks a lot Gaetano
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

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