Our group strives to make its software accessible to the biomedical community through a variety of training opportunities, workshops, classes, presentations and demonstrations. For those who cannot attend these training events, we post and maintain tutorials that scientists can work through at their own pace, as a means of learning the best use of the VMD and NAMD software packages. Some tutorials also introduce use of the software for scientific research, e.g., in case of tutorials introducing Steered Molecular Dynamics.

This section offers tutorials on tools created by our group, and some select tutorials from other groups. Proceeding through a tutorial requires the latest version of the software it addresses, and may also require files be placed in particular locations on one's computer first. Most of the tutorials are usable on Windows, Mac, and Unix/Linux platforms.

Be sure you have the latest version of VMD.

• VMD Molecular Graphics (html) (pdf, 1.2M) (required tutorial files [.tar.gz, 45.3M], [.zip, 45.3M], individual files)
  Participants build an image of ubiquitin whilst 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.
  


• VMD Images and Movies Tutorial (html) (pdf, 5.6M) (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.
  
 
• Aquaporins with the VMD MultiSeq Tool (html) (pdf, 7.9M) (required tutorial files [.tar.gz, 151M], [.zip, 151M], Individual files)
  For users seeking to learn about a specific use of VMD.  Introduces participants to the VMD MultiSeq Tool, which links protein structures to protein sequences and allows users to compare proteins in terms of structure and sequence.  The aquaporin family of membrane proteins, found in a wide range of species including humans, are used for a case study of the applications of the MultiSeq tool.  Requires VMD and the VMD MultiSeq Tool. Tutorial works on Windows, Mac, and Unix/Linux platforms.
   
• Visualization and Analysis of CPMD data with VMD (html)
  For users seeking to learn about a specific use of VMD.  Guides participants in using VMD for visualizing results from molecular dynamics and electronic structure calculations, as produced by the CPMD program.  Produced by Axel Kohlmeyer, Theoretische Chemie, Ruhr-Universität Bochum, Germany.
   
• Please also see the tutorials Evolution of Protein Structure Aspartyl-tRNA Synthetase, Simulation of Water Permeation through Nanotubes, Topology File Tutorial, and Stretching Deca-Alanine, each of which employ VMD.

Be sure you have the latest version of NAMD.

• NAMD Tutorial
  (html for Unix/Mac) (pdf for Unix/Mac, 7.9M)
  (html for Windows) (pdf for Windows, 6.4M)
  (required tutorial files (all platforms) [.tar.gz, 148M], [.zip, 148M], individual files (all platforms))
  Participants learn how to use NAMD to set up basic molecular dynamics simulations, and to understand typical NAMD input and output files, with an emphasis on such files for protein energy minimization and equilibration in water. Tutorial versions available for Windows, or Mac and Unix/Linux platforms.
  
  
• NAMD Paper
  The physical concepts behind NAMD along with the programs design and algorithms are described in this publication that we recommend highly for study along with working through the above NAMD tutorial
  Scalable molecular dynamics with NAMD. James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Journal of Computational Chemistry, 26:1781-1802, 2005. Download full text: PDF ( 977k)
   
• A Tutorial to Set Up Alchemical Free Energy Perturbation Calculations in NAMD (pdf, .1M) (required tutorial files [.zip, 487k])
  For users seeking to learn about a specific use of NAMD.  Discusses setting up the system and calculations needed for free energy calculations of alchemical transformations within NAMD.  Produced by Surjit B. Dixit, Jerome Henin, and Christophe Chipot, Institute Nanceien de
   
• A Tutorial to Set Up Adaptive Biasing Force Calculations in NAMD (pdf, .1M) (required tutorial files [.zip, 487k])
  For users seeking to learn about a specific use of NAMD.  Discusses setting up the system and calculations needed for adaptive biasing force calculations of conformational transitions within NAMD.  Produced by Jerome Henin, and Christophe Chipot, Institute Nanceien de Chimie Moleculaire, Universite Henri Poincare.
   
• Building Gramicidin A (html)
  A brief guide on setting up and equilibrating a molecular dynamics simulation, using the Gramicidin A system embedded in a POPE membrane, surrounded by water.
   
• Please also see the tutorials Simulation of Water Permeation through Nanotubes and Stretching Deca-Alanine, each of which employ NAMD.

The following tutorials each require one or more software packages to complete; account for the software requirements before attempting to proceed. 

• Parameterizing a Novel Residue (html) (pdf, 2.5M)
  (html for Linux) (pdf for Linux, 2.5M)
  (required tutorial files (all versions) [.tar.gz, 24.2M], [.zip, 24.2M], individual files (all versions))
  Takes participants through a comprehensive example of how one investigates, sets up, and simulates a small nonstandard ligand bound to a protein system; specifically, the glutaminase subunit of the hisH-hisF system and determining the parameters for the non-standard residue. Requires VMD, NAMD, and Spartan. Tutorial works on Windows, Mac, and Unix/Linux platforms.
   
• Evolution of Biomolecular Structure: Class II tRNA-Synthetases and tRNA (pdf, 3.0M) (required tutorial files [.tar.gz, 171M], [.zip, 171M], individual files)
  A tutorial that uses structural and sequence alignment to learn about the evolution of tRNAases.  Requires VMD and the VMD MultiSeq Tool. Tutorial works on Windows, Mac, and Unix/Linux platforms.
   
• Sequence Alignment Algorithms (pdf, 1.6M) (required tutorial files [.tar.gz, 570k], [.zip, 811k], individual files)
  Introduces participants to bioinformatics, the statistical analysis of protein sequences and structures to understand their function and predict structures when only sequence information is available. Requires Needleman-Wunsch alignment programs. Tutorial designed to work on the Mac platform only.
   
• Topology File Tutorial (html) (pdf, 4.4M ) (required tutorial files [.tar.gz, 11.2M], [.zip, 11.2M], individual files)
  Guides users in how to create topology and parameter information needed for molecular dynamics simulations when it otherwise doesn't exist, by using existing topology information for other molecules without the need for new parameter development.  Requires VMD, NAMD suggested as well. Tutorial works on Windows, Mac, and Unix/Linux platforms.
• User-Defined Forces in NAMD (html) (pdf, 3.0M ) (required tutorial files [.tar.gz, 293M], [.zip, 293M], individual files)
  This tutorial is designed to guide users of VMD and NAMD in the use of the tclForces and tclBC scripts. These script-based facilities simplify the process of adding complex forces to systems and implementing boundary conditions. Tutorial works on Windows, Mac, and Unix/Linux platforms.
• Bionanotechnology Tutorial (html) (pdf, 2.7M) (required tutorial files [.tar.gz, 189M], [.zip, 186M], individual files)
  This tutorial is designed to guide users of VMD and NAMD in all the steps required to set up a molecular dynamics simulation of a bionanotechnology device. Tutorial works on Windows, Mac, and Unix/Linux platforms.

Interactive Molecular Dynamics Tutorials

• For a brief introduction to running interactive molecular dynamics simulations, see the documentation here.
   
• Stretching Deca-Alanine (html) (pdf, 1.8M) (required tutorial files [.tar.gz, 5.3M], [.zip, 5.3M], individual files)
  Provides participants with an introduction of interactive molecular dynamics and steered molecular dynamics simulations, and to the calculation of potential mean force from trajectories obtained with steered molecular dynamics simulations.  Requires VMD and NAMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.
   
• Simulation of Water Permeation through Nanotubes (html) (pdf, 381k) (required tutorial files [.tar.gz, 39.8M], [.zip, 39.8M], individual files)
  Investigates the permeation of water through nanotubes, as a model for transmembrane permeation of substrates through channels.  Requires VMD and the AutoIMD extension to VMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.

Steered Molecular Dynamics Tutorials

• Please also see the NAMD Tutorial and the Stretching Deca-Alanine tutorial for content on steered molecular dynamics.

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These are some additional resources that have been used in TCBG Workshops.

• Emacs reference card (pdf)
• Vi reference card (pdf)
• Mac OSX Primer (html) (pdf)
• Unix Primer (html) (pdf)

• Tutorial-l mailing list
• Archive of tutorial-l mailings