VMD-L Mailing List

From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Thu Feb 13 2014 - 04:42:45 CST

Yes, and as I suggested, better use the VTF format, which is significantly
simpler to produce than the PDB format. ;-)

Simple example. Put the following lines into a file "test.vtf" and load it
with VMD. It will create two atoms with the given values of beta and place
them at positions (1,1,1) and (2,2,2) in the first frame. 

----
atom 0 beta 0.3
atom 1 beta 0.6
timestep
1. 1. 1.
2. 2. 2.
----
Olaf
2014-02-13 10:28 GMT+01:00 Norman Geist <norman.geist_at_uni-greifswald.de>:
> As far as I know, the PDB format holds 2 columns that could be used for
> that, called "Beta" and "Occupancy". Otherwise you can set any value you
> want for those columns and for multiple user defined values from the TCL
> interface. So you could also read those information afterwards to you
> structure from any file and format you want. Afterwards you can use
> Coloring Method->Beta for instance to visualize.
>
> Norman Geist.
>
> > -----Ursprüngliche Nachricht-----
> > Von: Arham Amouie [mailto:erham65t_at_yahoo.com]
> > Gesendet: Donnerstag, 13. Februar 2014 09:51
> > An: Norman Geist
> > Cc: VMD Mailing List
> > Betreff: Re: AW: vmd-l: Simplest file format that includes atom color?
> >
> > 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?
> >
> >
> >
> >
> >
> >
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> >
> >  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?
> >
> >
> >
> >
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> >
> >  Thanks in
> >  advance
> >
> >
> >
> >
> >
> >  Arham
> >  Amouei
> >
> >
> >
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> >
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> >  aktiv.
> >
> >
> >
> >
> >
>
>
>
-- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607