VMD-L Mailing List

From: Arham Amouie (erham65t_at_yahoo.com)
Date: Thu Feb 13 2014 - 02:51:07 CST

I mean coloring by some physical quantity, like velocity, speed, potential energy, etc.

Thanks
Arham Amouei

--------------------------------------------
On Thu, 2/13/14, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:

 Subject: AW: vmd-l: Simplest file format that includes atom color?
 To: "'Arham Amouie'" <erham65t_at_yahoo.com>
 Cc: "VMD Mailing List" <vmd-l_at_ks.uiuc.edu>
 Date: Thursday, February 13, 2014, 9:50 AM
 
 
 #yiv5813604484 #yiv5813604484 --
   
  _filtered #yiv5813604484 {font-family:Helvetica;panose-1:2
 11 6 4 2 2 2 2 2 4;}
  _filtered #yiv5813604484 {panose-1:2 4 5 3 5 4 6 3 2 4;}
  _filtered #yiv5813604484 {font-family:Calibri;panose-1:2 15
 5 2 2 2 4 3 2 4;}
  _filtered #yiv5813604484 {font-family:Tahoma;panose-1:2 11
 6 4 3 5 4 4 2 4;}
 #yiv5813604484
 #yiv5813604484 p.yiv5813604484MsoNormal, #yiv5813604484
 li.yiv5813604484MsoNormal, #yiv5813604484
 div.yiv5813604484MsoNormal
         {margin:0cm;margin-bottom:.0001pt;font-size:12.0pt;}
 #yiv5813604484 a:link, #yiv5813604484
 span.yiv5813604484MsoHyperlink
         {color:blue;text-decoration:underline;}
 #yiv5813604484 a:visited, #yiv5813604484
 span.yiv5813604484MsoHyperlinkFollowed
         {color:purple;text-decoration:underline;}
 #yiv5813604484 span.yiv5813604484E-MailFormatvorlage17
         {color:#1F497D;}
 #yiv5813604484 .yiv5813604484MsoChpDefault
         {font-size:10.0pt;}
  _filtered #yiv5813604484 {margin:70.85pt 70.85pt 2.0cm
 70.85pt;}
 #yiv5813604484 div.yiv5813604484Section1
         {}
 #yiv5813604484
 
 
 
 
 Hi Arham,
 
   
 
 I suppose with „each atom can
 have its particular color“ you
 mean coloring by element? If so, the xyz format does already
 allow to mention
 the element of the atoms in the 1st column, see
 http://en.wikipedia.org/wiki/XYZ_file_format, and VMD should use
 it. Otherwise please explain more detailed.
 
 
 
   
 
 Norman Geist.
 
 
 
   
 
 
 
 
 
 
 
 Von:
 owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu]
 Im Auftrag von Arham
 Amouie
 
 Gesendet: Mittwoch, 12. Februar 2014 20:29
 
 An: vmd-l_at_ks.uiuc.edu
 
 Betreff: vmd-l: Simplest file format that includes
 atom color?
 
 
 
 
 
   
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 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
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                         
                                 
                         
                 
                         
                                 Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist
 aktiv.