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

Careful these pages are outdated unsupported archival copies

The aim of this tutorial is to help you using the program VMD for visualizing results from (first principles) molecular dynamics and electronic structure calculations, mainly done with the CPMD program, but also data from other codes like ESPRESSO/PWScf, GROMACS or Gaussian that can produce similar outputs are considered. It follows a close hands-on approach, so you will be provided with many examples and solutions to common problems. Most of the examples were conceived to satisfy specific needs in the Lehrstuhl für Theoretische Chemie at the Ruhr-Universität Bochum, but we try to not only show the solutions but also to describe the recipes. So we hope that the techniques described can not only be used to solve a particular problem, but are of more general use and can be translated to other, similar problems. Many of the examples should be adaptable with little effort to data created by other electronic structure or simulation programs. To help you getting started, most of the data and input files are available for download, so you in many cases, you will only need to adapt and/or combine the existing solution(s). Please note, however, that the following is assuming some background knowledge about using VMD. If you are new to VMD, you should start instead with the introductory tutorial on the VMD homepage.

CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory. It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimizations, Born-Oppenheimer MD, path integral MD, response functions, excited states and calculation of some electronic properties. For further information you can take a look at the CPMD consortium homepage at http://www.cpmd.org/.

Visual Molecular Dynamics (VMD) is a very powerful and flexible toolkit for visualization and analysis of molecular dynamics simulation data. Although it was initially developed with focus on large biomolecular systems, newer versions contain many features that make it a very attractive choice for visualizing results from CPMD and other electronic structure calculations. Further information can be found on the VMD homepage at http://www.ks.uiuc.edu/Research/vmd/. There also is a VMD Script Library with more examples of VMD scripting.

Part 1

Contents

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1.3. Notes
Most of the examples presented here assume, were tested with and may only run with VMD version 1.8.3 or later on a UNIX(TM)/Linux machine.

Contact axel.kohlmeyer@theochem.ruhr-uni-bochum.de if there are compatibility problems with newer versions of VMD or on other platforms. Any other form of feedback, e.g. corrections, enhancements, further examples, or new visualization problems, is also highly welcome.

Since the following pages mainly deal with visualization and animation of trajectory data, they will be filled with graphics and GIF-movies (total ~20MB). Although considerable effort has been put into reducing file sizes and splitting the webpage into several smaller pages, you may still consider downloading the single file PDF version (306 kByte) if you have a low bandwidth connection. Please note, that the conversion to pdf sometimes has problems with the preprocessed html code, so that the resulting pdf file here may be incomplete (everything is created from a single source). Please notify me in that case. After switching from html2ps to HTMLDOC errors have been considerably fewer, while the quality of the created pdf has improved a lot.

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

2005/01/03

Several new examples, tricks, hacks and utilities added. Some examples now also come with directions or inputs for ESPRESSO/PWScf. Reviewed some of html generation macros, added support for computed links between parts.

2004/07/06

Introduced sections for the start page and added this section, so that people know when and where to look for new stuff. Older changes taken from the CVS changelog.

2004/07/05

PDF file generation now uses HTMLDOC instead of html2ps. The PDF is looking much nicer now and generation is much faster and needs less memory. Also fixed a bunch of minor markup errors detected by htmldoc.

2004/05/21

Added example for 'cloning' a representation from one molecule to another (with an optional GUI) and how to hook up a Tk-GUI into the extension menu.

2004/05/16

Added example for calculating a 2d-Ramachandran distribution and how to draw the result as color-coded 3d-surface using triangle drawing primitives.
Added example for a hardcopy printing command.

2004/05/14

Added two new examples:
Banging two buckyballs together to illustrate the 'User' colorization method,
and an animated Isosurface (by cycling through the volumetric data sets) of a Hydrogen molecule shot trough Gold atoms.

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Part 1

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