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.

• Using VMD (html) (pdf, 1.6M) (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, 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, 4.6M) (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)



• Membrane Proteins Tutorial (pdf, 1.0M) (required tutorial files: reduced version [.tar.gz, 10.2M]; full version, [.tar.gz, 508M]*)
  Step by step tutorial for setting up and running molecular dynamics simulations of membrane proteins. Requires VMD, NAMD, and Solvate. Tutorial works on Unix/Linux platform. *Note: download of full version of files limited by bandwidth availability.
 
 
• 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 Chimie Moleculaire, Universite Henri Poincare.
   
• A Tutorial to Set Up Adaptive Biasing Force Calculations in NAMD (pdf , 1.6 M) (required tutorial files [tar.gz, 1.6 M] )
  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 Translation: Class-I aminoacyl-tRNA synthetases (pdf, 6.4 MB) (required tutorial files [tar.gz, 268 MB])
  This tutorial makes use of the MultiSeq bioinformatic analysis environment to explore the evolution of the class I aminoacyl-tRNA synthetases, which 'charge' transfer RNA (tRNA) with the correct amino acid. It is intended to be an introduction to MultiSeq, and no prior knowledge of MultiSeq is required. Topics covered include: BLAST searches, multiple sequence alignments, structural alignments, and distance-based phylogenetic trees.
   
• Evolution of Translation: EF-Tu (pdf, 3.7 MB) (required tutorial files [tar.gz, 284 MB])
  This tutorial is intended to be a advanced lesson in the MultiSeq bioinformatic analysis environment, and we recommend the user first go through the Class-I Aminoacyl-tRNA synthetases tutorial prior to attempting this one. In it you will explore the evolutionary relationship of the elongation factor Tu, which ferries 'charged' tRNA from the sythetase to the ribosome. Topics covered include: profile-profile alignments, maximum likelihood phylogenetic trees with RAxML, and scripting with MultiSeq.
   
• Evolution of Translation: Ribosome (pdf, 1.3 MB) (required tutorial files [tar.gz, 41 MB])
  This tutorial leads the reader through major features of the ribosome, the primary translation machinery of the cell. Interactions with the elongation factors, mRNA, and tRNA are explored, as are newly discovered 'sequence signatures' between bacterial and archaeal ribosomes. These signatures constitute much of the evolutionary distance between these two domains of life, and their role in antibiotic resistance is explored. We recommend the reader first complete the Class-I aminoacyl-tRNA synthetase tutorial prior to attempting this one.
   
• 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.



• Shape-Based Coarse Graining (html) (pdf, 2.4M) (required tutorial files, [.zip, 6.5M], individual files)
  This tutorial presents one method of coarse-graining, called shape-based coarse-graining, which has been quite successful in a number of applications. In this method, a small number of CG beads are used to represent overall shapes of proteins or lipid membranes, with typical ratio of 200-500 atoms per bead. Requires VMD, NAMD, and a plotting program. 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, 419k) (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