These tutorials focus on VMD-specific features, although many others 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, 26.0M) (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.
• 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.
• Short and topical VMD tutorials: Publication figure rendering with Tachyon • Publication figure rendering using NVIDIA Gelato • VMD outline rendering style inspired by the work of D. Goodsell • Creating interactive 3-D PDF documents with VMD and Acrobat3D • Coloring molecules by electrostatic potential, and other volumetric data • Selecting atoms by volumetric density values
• Video lecture: an introductory video "Introduction to VMD Molecular Visualization and Analysis" recorded by Dr. Emad Tajkhorshid in November, 2007 is available here.

These tutorials focus on NAMD specifically, although many others utilize it as well. Be sure you have the latest version of NAMD.

• NAMD Tutorial
  (html for Unix/Mac) (pdf for Unix/Mac, 8.0M)
  (html for Windows) (pdf for Windows, 6.5M)
  (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)
• Video lecture: an video reviewing the conceptual foundations of NAMD, "Statistical Mechanics of Proteins" as recorded by Dr. Klaus Schulten in November 2010 is available here.
• User-Defined Forces in NAMD (html) (pdf, 4.3M ) (required tutorial files [.tar.gz, 306M], [.zip, 306M], 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.

Interactive Molecular Dynamics Tutorials

• For a brief introduction to running interactive molecular dynamics simulations, see the documentation here. The tutorials on Simulation of Water Permeation through Nanotubes and on Stretching Deca-Alanine both utilize IMD.
   

Steered Molecular Dynamics Tutorials

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

The following tutorials cover multiple free-energy and potential-of-mean-force calculation methods using NAMD. 

• A Tutorial on Alchemical Free Energy Perturbation Calculations in NAMD (pdf, 651k) (required tutorial files [.tar.gz, 2.1M], [.zip, 2.1M], individual files)
  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. 
• A Tutorial on Adaptive Biasing Force Calculations in NAMD (pdf, 1.1M) (required tutorial files [.tar.gz, 38.4M], [.zip, 38.4M], individual files)
  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. 
• Stretching Deca-Alanine (html) (pdf, 1.4M) (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.
• Forcing Substrates Through Channels (pdf, 945k) (required tutorial files [.tar.gz, 54.2M], [.zip, 54.2M], individual files)
  In this tutorial, applications of steered molecular dynamics and adaptive biasing forces to the ammonium transporter AmtB are explored. Steered molecular dynamics will be used first to gain an approximate knowledge of the permeation pathway and the barriers along it. Then, the potential mean of force for ammonia in the central region of the channel is calculated using adaptive biasing forces. The appropriate choice of parameters and potential difficulties will also be discussed. Requires VMD, NAMD, and a plotting program.

The following tutorials focus on sequence and structure analysis primarily through the VMD tool, Multiseq. They may also require one or more additional software packages to complete; account for the software requirements before attempting to proceed. 

• Aquaporins with the VMD MultiSeq Tool (html) (pdf, 1.9M) (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.
• 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.  

The following tutorials address applications of simulation techniques to inorganic devices for various purposes.  

• Bionanotechnology Tutorial (html) (pdf, 2.9M) (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.
• Simulation of Water Permeation through Nanotubes (html) (pdf, 435k) (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.
• Modeling Nanopores for Sequencing DNA (pdf, 15M), (required tutorial files, [.tar.gz, 277M])
  Using nanopores to sequence DNA rapidly and at a low cost has the potential to radically transform the field of genomic research. However, despite all the exciting developments in the field, sequencing DNA using a nanopore has yet to be demonstrated. Among the many problems that hinder development of the nanopore sequencing methods is the inability of current experimental techniques to visualize DNA conformations in a nanopore and directly relate the microscopic state of the system to the measured signal. We have recently shown that such tasks could be accomplished through computation. This tutorial provides step-by-step instructions of how to build atomic scale models of biological and solid-state nanopore systems, using the molecular dynamics method to simulate the electric field-driven transport of ions and DNA through the nanopores, and analyze the results of such computational experiments. The tutorial is designed for use on Unix/Linux platforms, but will work on any system with working installations of VMD and NAMD.

The following tutorials cover specific methods for, e.g., force-field development of non-standard residues, simulation of membrane proteins, and other advanced topics. 

• 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.  
• 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.
• 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.
• 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.

• 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.
• Molecular Dynamics Flexible Fitting (MDFF) (html) (pdf, 1.3M) (required tutorial files [.tar.gz, 98.2M] [.zip, 98.2M], individual files)
  This tutorial describes how to flexibly fit atomic structures into density maps using the MDFF method. This method can be used to obtain atomic models of macromolecular complexes by combining X-ray structures and cry-electron microscopy maps. Requires VMD and NAMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.
• Timeline: a VMD Plugin for Trajectory Analysis (html) (pdf, 2.5M) (required tutorial files [.tar.gz, 58.0M] [.zip, 58.0M], individual files)
  Timeline creates an interactive 2D box-plot -- time vs. structural component -- that can show detailed structural events of an entire system over an entire MD trajectory. Events in the trajectory appear as patterns in the 2D plot. The plugin provides several built-in analysis methods, and the means to define new analysis methods.

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