VMD-L Mailing List

From: Arham Amouie (erham65t_at_yahoo.com)
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

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

 Subject: Re: vmd-l: Simplest file format that includes atom color?
 To: "Arham Amouie" <erham65t_at_yahoo.com>, "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
 Date: Thursday, February 13, 2014, 8:16 AM
 
 
     On 2/12/2014 2:28 PM,
 Arham Amouie
       wrote:
 
     
     
       
         
           
             
               
                 
                   Hello
                   
 
                   
                   I've
 
                     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
 particular
                     color. I used csv format of ParaView for
 this
                     reason, but ParaView doesn't work
 fast for me. What
                     is the easiest solution in VMD?
                   
 
                   
                   Thanks
                     in advance
                   Arham
                     Amouei
                 
               
             
           
         
       
     
     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 jpotoff_at_wayne.edu
 Associate Professor and Director of Early Engineering
 Programs
 Department of Chemical Engineering and Materials Science
 Wayne State University 5050 Anthony Wayne
 Dr
 Detroit, MI 48202
 http://potoff1.eng.wayne.edu
 ======================================================================