The tutorials below focus on VMD-specific features, although many other tutorials utilize VMD as well. Be sure you have the latest version of VMD.

  • Using VMD (html) (pdf, 1.4M) (required tutorial files [.tar.gz, 44.9M], [.zip, 44.9M], individual files)
    Participants build an image of ubiquitin while becoming familiar with basic VMD commands. Additionally, participants learn how to look for interesting structural properties of proteins using VMD. Tutorial works on Windows, Mac, and Unix/Linux platforms. The previous version of the tutorial can be found here.
  • VMD Images and Movies Tutorial (html) (pdf, 26.1M) (required tutorial files [.tar.gz, 88.0M], [.zip, 88.0M], individual files)
    This tutorial is designed to give users of VMD an introduction to advanced techniques for making custom images and movies. The first section looks at how to use features such as resolution, color, and material, depth perception, and volumetric data to produce effects and enhancements for still images. The second part demonstrates how to work with trajectories, by using techniques such as smoothing trajectories, showing multiple frames at once, and making atom selections "follow" a trajectory. It also shows how to create a movie file from a trajectory using VMD's Movie Maker plugin. Tutorial works on Windows, Mac, and Unix/Linux platforms.
  • Structure Check (html) (pdf, 720k) (required tutorial files [.tar.gz, 762k] [.zip, 753k], individual files)
    This tutorial describes two VMD plugins that can be used to detect and correct certain structure errors, namely chirality and cis peptide bonds. The plugins can also be used to prevent these errors from occuring in simulations with NAMD. Requires VMD and NAMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.
  • VMD Quantum Chemistry Visualization Tutorial (pdf, 2.0M) (required tutorial files [.zip, 600k], individual files)
    VMD can be used to load files that contain quantum mechanics (QM) data such as GAMESS log files and Molden files. With QM data loaded, VMD can display molecular orbitals, as well as access the calculated energy levels and various other data present in the loaded files. In this tutorial output from the GAMESS program will be used to provide input for visualization of QM Data using VMD. Requires VMD, GAMESS.
  • GPU Accelerated Molecular Dynamics Simulation, Visualization, and Analysis (pdf, 443K) (required tutorial files [.tar.gz, 1.32GB]*)
    This tutorial will demonstrate how to use features in NAMD and VMD to harness the computational power of graphics processing units (GPUs) to accelerate simulation, visualization and analysis. Requries VMD, NAMD. Works on Windows, Mac, and Linux. *Note: download of files may be limited by bandwidth availability.
  • Video lecture: an introductory video "Introduction to VMD Molecular Visualization and Analysis" recorded by Dr. Emad Tajkhorshid in November, 2007 is available here.

  Introduction to VMD Molecular
Visualization and Analysis
  Emad Tajkhorshid, November 2007

Tutorials and Resources

References: Emacs reference card (pdf) • Vi reference card (pdf) • Mac OSX Primer (html) (pdf) • Unix Primer (html) (pdf)
Contacts: Suggest an idea for a tutorialTutorial-l mailing listarchive of tutorial-l mailings
Case studies: water DNA lipid bilayers BPTIubiquitin myoglobinaquaporin ion channels titin lh2

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