From: Arham Amouie (
Date: Thu Feb 13 2014 - 05:27:45 CST

Thanks. I don't know PBD format very well, but actually I guess it's too complicated for my need.

Arham Amouei

On Thu, 2/13/14, Jeffrey Potoff <> wrote:

 Subject: Re: vmd-l: Simplest file format that includes atom color?
 To: "Arham Amouie" <>, "" <>
 Date: Thursday, February 13, 2014, 8:16 AM
     On 2/12/2014 2:28 PM,
 Arham Amouie
                     written a MD code for EAM potentials.
 The typical
                     number of atoms is of the order of 1
 million. This
                     code saves the positions in xyz files
 and I use VMD
                     for visualization. Now, I'm going to
 change the
                     output, so that each atom can have its
                     color. I used csv format of ParaView for
                     reason, but ParaView doesn't work
 fast for me. What
                     is the easiest solution in VMD?
                     in advance
     If you output as PDB, you can color based on atom
 name.  You can
     also use the beta and occupancy fields for more options
 with respect
     to atom coloring.
 Jeffrey J. Potoff
 Associate Professor and Director of Early Engineering
 Department of Chemical Engineering and Materials Science
 Wayne State University 5050 Anthony Wayne
 Detroit, MI 48202