Subject: CCL: summary on MD-trajectories animations

From: "Artem R. Oganov" <[email-masked]>
Date: Mon, 8 Nov 1999 21:58:23 -0000

Dear CCL'ers,
 
My original enquiery was :
I am looking for a program to animate MD trajectories, with polyhedral
representation of crystal structures. I shall be grateful for any
suggections, and summarise them. Also, does anyone know what is the Web-site
of Babel?
Many thanks to Keith Refson, Robert Best and Ricardo Grau Crespo, whose replies (slightly shortened) I summarise below:

Keith Refson :
Cerius 2 does this I think.  But perhaps you are looking for something
free.  You probably need the MD modules as well as the crystal builder.
AVS : there's Larry Finger's "crystal" AVS module which can be used for
polyhedral representations.  And you can use AVS to animate.  However
it has it's own unique structure format files.

On a Win32 PC there's MSI's free WebLab viewer which I believe will do 
this.  I'm not aware of anything free for unix which does.

Babel is pretty useless at converting between periodic crystal
structure files and usually loses all symmetry and unit cell
information.  I have written some perl scripts for converting between
PDB/Schakal and CASTEP formats if you are interested.
They are in ftp://ftp.earth.ox.ac.uk/pub/keith/cteptouts.tar.gz

Robert Best :  
A good program for displaying trajectories and doing analysis is gopenmol,
available from http://laaksonen.csc.fi/gopenmol. Although the emphasis 
is on analysis of amorphous systems, there is a facility for drawing cubic
cells, and you can draw any kind of cell using the built-in tcl scripting.
Of course there are crystallographic programs which make the cell drawing
easier, but I don't know of any that have the ability to display 
trajectories as well.

Ricardo Grau Crespo :
Babel lives in a lot of places on the net,
but the "official" distribution site is
http://www.eyesopen.com/babel.html

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Artem R. Oganov,                                                                 
Doctorate Student in Crystallography and Mineral Physics, 
Dept. of Geological Sciences,                                             
University College London,                                                   
Gower Street,                                                                       
London WC1E 6BT,                                                            
U.K.                                                                                     
E-mail : [email-masked]                                              
Tel. : +44 (0)171-419-3449        Fax : +44 (0)171-387-1612                                                  
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