From: Axel Kohlmeyer (
Date: Mon Dec 09 2013 - 08:13:35 CST

It should be possible to do this by creating a custom material and using a trace on vmd_frame to modify its transparency based on the current frame number. I don't have access to machine with vmd installed to produce and example script, but there are some examples posted to the list and on the web that do somewhat similar things.

------Original Message------
From: Gaetano Calabró
Subject: vmd-l: Change transparency along a trajectory
Sent: Dec 9, 2013 12:55 PM

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.
Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.