Theoretische Chemie, Ruhr-Universität Bochum,Germany http://www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html

Homepage Axel Kohlmeyer

Visualization and Analysis of Quantum Chemical and Molecular Dynamics Data with VMD Part 8

    10. Credits

    11. Downloads

    12. Script distribution policy


    Part 7     Start     Contents

This page was compiled by

Axel Kohlmeyer,
Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum,
axel.kohlmeyer@theochem.ruhr-uni-bochum.de

Additional simulation data was contributed by

Holger Langer, Volker Kleinschmidt, Marcel Baer
Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum
Heshe Peshkin

Helpful suggesions and encouragement

John E. Stone, Dominik Marx, Roger Rousseau, Volker Kleinschmidt, Holger Langer, Eduard Schreiner, Amalendu Chandra, Marcel Baer

VMD

Humphrey, W., Dalke, A. and Schulten, K.,
VMD - Visual Molecular Dynamics" J. Molec. Graphics 1996, 14.1, 33-38.
http://www.ks.uiuc.edu/Research/vmd/

CPMD

Copyright IBM Corp © 1990-2005,
Copyright MPI für Festkörperforschung Stuttgart © 1997-2001.
http://www.cpmd.org/

ESPRESSO / PWscf

Stefano Baroni, Stefano de Gironcoli, Andrea Dal Corso (SISSA, Trieste),
Paolo Giannozzi (Scuola Normale, Pisa) and others.
http://www.pwscf.org/

Gaussian 98 (Revision A.11)

M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. G. Johnson, W. Chen, M. W. Wong, J. L. Andres, M. Head-Gordon, E. S. Replogle and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 1998.
Copyright © 1988, 1990, 1992-1999, Gaussian, Inc.,
and copyright © 1983, Carnegie Mellon University
http://www.gaussian.com/

Tachyon

Copyright © 1994-2005 John E. Stone
http://jedi.ks.uiuc.edu/~johns/raytracer/

Raster3D

Merritt & Bacon (1997) Meth. Enzymol. 277, 505-524.
http://www.bmsc.washington.edu/raster3d/

ImageMagick

Copyright © 1999-2004 ImageMagick Studio LLC.
http://www.imagemagick.org/

Gifsicle

Copyright © 1997-2003 by Eddie Kohler.
http://www.lcdf.org/gifsicle/

htmldoc

Copyright © 1997-2004 by Easy Software Products.
http://www.easysw.com/htmldoc/

Mjpegtools

by Rainer Johanni, Gernot Ziegler, Andrew Stevens, Bernhard Praschinger, Ronald Bultje, Xavier Biquard, Matthew Marjanovic, pHilipp Zabel, Kawamata/Hitoshi, Stefan Fendt, Scott Moser, Shawn Sulma, Mike Bernson, James Klicman
http://mjpeg.sourceforge.net/

WML -- Website META Language

Copyright © 1996-2001 Ralf S. Engelschall
Copyright © 1999-2001 Denis Barbier
http://thewml.org/

If you want to cite or bookmark this page please use the URL
http://www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html
as the underlying link might change in the future.

The following files and archives are available for download:

	(20.960 MByte)	cpmd-vmd-examples.tar.gz	All example files as gzipped tar archive
	(20.752 MByte)	cpmd-vmd-examples.zip	All example files as zip archive
	(0.300 MByte)	cpmd-vmd.pdf	A PDF version of the full document

The scripts linked to on this page are made available free of charge for personal use. They still are copyrighted by the author(s) mentioned in the individual files. They may not be used in any commercial software without prior agreement of the author(s).

These scripts are distributed in the hope that they will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

All trademarks and registered trademarks are the properties of their respective holders.

All data files used for the examples presented here are available for download. You can look a all the files, if you follow the link to the files section.

Top of Page

Part 7

Start

Full Table of Contents


1. Introduction
     1.1. About this Tutorial
     1.2. About the Programs
     1.3. Notes
     1.4. Citation / Bookmark
     1.5. Recent Changes
2. Table of Contents
3. Preparation and Installation Issues
     3.1. Customizing the VMD Setup
     3.2. Predefining Additional Items
     3.3. Extending the Script and Plugin Search Path
4. Loading and Displaying Configurations and Trajectories
     4.1. Loading a Single Geometry
     4.2. Creating a Visualization
     4.3. Saving and Re-using a Visualization
     4.4. Viewing a Trajectory
     4.5. How to Show Breaking and Formation of Bonds
     4.6. Adding Graphics to a Visualization
5. Adding Dynamic Graphics to a Trajectory
     5.1. Adding a Progress Bar for the Elapsed Time
     5.2. Display the Total Dipole Moment of the Simulation Cell
     5.3. Visualizing Changing Atom Properties with Color
     5.4. Modify an Atom Property Dynamically from an External File
6. Dynamic Atom Selection
     6.1. Display a Changing Number of Molecules
     6.2. Keeping Atoms or a Molecule in the Center and Aligned
     6.3. Modify a Selection During a Trajectory
     6.4. Using the User Field for Computed Selections
     6.5. Tracing a Dynamic Property
7. Visualizing Volumetric Data from Cube-Files
     7.1. Electron Density and Electrostatic Potential
     7.2. Canonical and Localized Orbitals
     7.3. Electron Localization Function (ELF)
     7.4. Manipulation of Cube Files / Response to an External Potential
     7.5. Bulk Systems
     7.6. Animations with Isosurfaces
     7.7. Volumetric data from Gaussian
8. Using Data Processing to Tailor Data for VMD
     8.1. Visualizing Path-Integral Trajectories
     8.2. Extracting the Geometry Information from old CPMD Output Files
     8.3. Removing Unneeded Parts From a Cube File
     8.4. Extract Some Coordinates with Bounding Box Information
     8.5. Creating 3d-Ramachandran Histograms
9. Misc Tips and Tricks
     9.1. Collected 'draw' Extensions
     9.2. Using a Different Default Visualization
     9.3. Changing the Default vdW Radii
     9.4. Reloading the Current Trajectory
     9.5. Visualize a Trajectory With a Changing Number of Atoms or Bonds
     9.6. Set the Unit Cell Information for a Whole Trajectory
     9.7. Directly Print the Current Visualization
     9.8. Transferring a Visualization from a Molecule to Others
     9.9. Adding a TCL-Plugin to the Extensions Menu
     9.10. Turn Off Output in Analysis Scripts
     9.11. Automatically Turn on TCL mode in (X)Emacs for .vmd Files
10. Credits
11. Downloads
12. Script distribution policy

Theoretische Chemie, Ruhr-Universität Bochum,Germany http://www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html	Homepage Axel Kohlmeyer
Disclaimer   /   E-mail to the webmaster of this hompage: webmaster@theochem.ruhr-uni-bochum.de Source File: index.wml (Thu Aug 25 19:02:51 2005) ($Revision: 1.44 $) Translated to HTML: Mon Oct 10 00:05:54 2005