[CPMD-list] Vizualization path integral dynamics

[Axel Kohlmeyer]

On Mon, 18 Apr 2005, Przemyslaw Dopieralski wrote:

PD> 
PD> Hello

dear przemyslaw,

PD> I begin vizualization of path integral dynamic with vmd 1.8.3 liunux ver.
PD> (description on Axel Kohlmayer site). I used Axel's script traj2xyz.pl.
PD> At this moment OK. But now I don't know what next. I've got new TRAJECTORY
PD> with X but vmd doesn't read it - or maybe I did something wrong. My NEW
PD> TRAJECTORY with X looks good - I saw examples on Axel's Kohlmayer webpage.

i assume, you are referring to part 6, point 8.1 of the tutorial, i.e.:
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part6.html#chap8_sect1

the example is just a demontration, that you have to adapt to your
specific needs. if you want to get the same or a similar visualization, 
you can download the nh3-pimd.vmd script, change the line

mol new {nh3-pimd.xyz} type xyz waitfor all

so it corresponds to the filename of your trajectory and then
load the modified vmd script via 'File->Load State...'.

you have to realize, that VMD was initially conceived to represent
biomolecules and has thus no knowledge or internal heuristics for
data from ab initio calculations. so for meaningful visualization 
of CPMD results, you need to build custom visualizations and add
a little additional script magic here and there. to provide some 
examples and inspiration for that is the main idea of the tutorial.
there is _no_ way to have a ready-to-use script for all problems,
you have to see it more like a toolkit or a starting point.

regards,
	axel.

p.s.: if anybody has suggestions, improvements or visualization
problems, that are not covered by the tutorial, please let me 
know. i'm always looking for new challenges... ;-)

PD> 
PD> What shoud I do now?
PD> 
PD> Best regards,
PD> Przemyslaw Dopieralski
PD> University of Wroclaw
PD> 
PD> 
PD> 
PD> 
PD> _______________________________________________
PD> CPMD-list mailing list
PD> CPMD-list at cpmd.org
PD> http://cpmd.org/mailman/listinfo/cpmd-list
PD> 
PD> 

-- 

=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.