From: Adkins, Laura R (
Date: Wed May 11 2011 - 19:17:05 CDT

I apologize if this issue has been addressed previously (in a way accessible to a non-expert programmer) and would be happy to be directed to any previous discussion.

That said, I'm using VMD to run DLPOLY2 history files, and I've reassigned the names of the atoms in different timesteps to reflect their coordination within the system. For example, some of the oxygen is relabeled as iron in various timesteps of the run. I want these atoms to change color, throughout the trajectory run.

I've tried using 'update every frame' but it doesn't work. I've tried coloring the atoms by name (first letter of the atom), and element. When I used element, all the atoms were the same color. So I converted the file to XYZ format, and when I used element as the coloring method again, I got diverse colors, as appropriate. Still, the atoms did not change color when the ID changed with the timestep.

When I isolate timesteps to input them into VMD separately, the atom colors clearly correlate with the atom identities as they vary, but I'm dealing with 600 frames, and don't relish the task of sorting through the resultant files.

Laura Adkins