TCBG 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 speed, as a means of learning the best use of the VMD and NAMD software packages. The page below offers tutorials on tools created by TCBG, and some tutorials from other groups. Proceeding through a tutorial requires a copy of the tutorial text (in pdf or html format), tutorial files in place on the user's computer, and installation of VMD, NAMD, and other required software as documented at the start of each tutorial. Most of the tutorials are usable on Windows, Mac, and Unix/Linux platforms. It is suggested that you use the latest machine you have available; while the tutorials will run on older machines, it may be slow going.

Using the tutorials:




Tutorial topics: VMD TutorialsNAMD TutorialsFree Energy MethodsBioinformaticsBionanotechnologySpecialized Topics


VMD Tutorials

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


VMD Tutorial
Using VMD:
  • 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.
  • Instructions: [html] [pdf, 1.4M]
  • Required tutorial files: [.tar.gz, 44.9M], [.zip, 44.9M], [individual files]




VMD Images and Movies Tutorial
VMD Images and Movies Tutorial:
  • 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.
  • Instructions: [html] [pdf, 26.1M]
  • Required tutorial files: [.tar.gz, 88.0M], [.zip, 88.0M], [individual files]




Structure Check
Structure Check:
  • 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 occurring in simulations with NAMD. Requires VMD and NAMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.
  • Instructions: [html] [pdf, 720k]
  • Required tutorial files: [.tar.gz, 762k] [.zip, 753k], [individual files]




VMD Quantum Chemistry Visualization Tutorial
VMD Quantum Chemistry Visualization Tutorial:
  • 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.
  • Instructions: [pdf, 2.0M]
  • Required tutorial files: [.zip, 600k], [individual files]




Visualization and Analysis of CPMD data with VMD
Visualization and Analysis of CPMD data with VMD
  • 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.
  • Instructions: [html] [pdf]
  • Required tutorial files: [individual files]




Short and topical VMD tutorials:
Video lectures: an introductory video, "Introduction to VMD Molecular Visualization and Analysis", recorded by Dr. Emad Tajkhorshid in November, 2007 is available here.

NAMD Tutorials

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


NAMD Tutorial
NAMD Tutorial:



User-Defined Forces Tutorial
User-Defined Forces in NAMD:
  • 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.
  • Instructions: [html] [pdf, 4.3M]
  • Required tutorial files: [.tar.gz, 306M], [.zip, 306M], individual files




Interactive Molecular Dynamics: Steered Molecular Dynamics Tutorials NAMD Paper
  • The physical concepts behind NAMD along with the program's 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)


Free-Energy Methods

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


FEP Tutorial
A Tutorial on Alchemical Free Energy Perturbation Calculations in NAMD:
  • 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.
  • Instructions: [pdf, 651k]
  • Required tutorial files: [.tar.gz, 2.1M], [.zip, 2.1M], [individual files]




ABF Tutorial
A Tutorial on Adaptive Biasing Force Calculations in NAMD:
  • 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.
  • Instructions: [pdf, 1.4M]
  • Required tutorial files: [.tar.gz, 38.5M], [.zip, 38.5M], [individual files]




IMD Tutorial
Stretching Deca-Alanine:
  • This tutorial will introduce the user to interactive molecular dynamics (IMD) and steered molecular dynamics (SMD) simulations, and to the calculation of potential of mean force (PMF) from trajectories obtained with SMD simulations. Requires VMD and NAMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.
  • Instructions: [html] [pdf, 1.4M]
  • Required tutorial files: [.tar.gz, 5.3M], [.zip, 5.3M], [individual files]




Forcing Substrates Through Channels
Forcing Substrates Through Channels:
  • 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.
  • Instructions: [pdf, 945k]
  • Required tutorial files: [.tar.gz, 54.2M], [.zip, 54.2M], [individual files]


Bioinformatics

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/MultiSeq Tutorial
Aquaporins with the VMD MultiSeq Tool:
  • 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.
  • Instructions: [html] [pdf, 1.9M]
  • Required tutorial files: [.tar.gz, 151M], [.zip, 151M], [individual files]




Evolution of Translation Class I
Evolution of Translation: Class-I aminoacyl-tRNA synthetases:
  • 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.
  • Instructions: [pdf, 6.4 MB]
  • Required tutorial files: [tar.gz, 268 MB]]




Evolution of Translation: EF-Tu
Evolution of Translation: EF-Tu:
  • This tutorial is intended to be an 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.
  • Instructions: [pdf, 3.7 MB]
  • Required tutorial files: [tar.gz, 284 MB]




Evolution of Translation: Ribosome
Evolution of Translation: Ribosome:
  • 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.
  • Instructions: [pdf, 1.3 MB]
  • Required tutorial files: [tar.gz, 41 MB]




Dynamical Network Analysis
Dynamical Network Analysis:
  • This tutorial introduces several network analysis methods for examining dynamic signaling in biomolecular systems. The NetworkView plugin to VMD is used to display and manipulate representations of the networks projected onto the underlying molecular structures. The tutorial is designed such that it can be used by both new and experienced users of VMD, however, it is highly recommended that new users go through the "Using VMD" tutorial in order to gain a working knowledge of the program. Users will also need to download the free Carma software program for the tutorial. This tutorial should take about two hours to complete in its entirety.
  • Instructions: [pdf, 4M]
  • Required tutorial files: [tar.gz, 192M]; network analysis code [tar.gz, 27M]




Sequence Alignment Algorithms
Sequence Alignment Algorithms:
  • 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.
  • Instructions: [pdf, 1.6M]
  • Required tutorial files: [.tar.gz, 570k], [.zip, 811k], [individual files]



Bionanotechnology

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


Bionanotechnology Tutorial
Bionanotechnology Tutorial:
  • 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.
  • Instructions: [html] [pdf, 2.9M]
  • Required tutorial files: [.tar.gz, 189M], [.zip, 186M], [individual files]




Simulation of Water Permeation through Nanotubes
Simulation of Water Permeation through Nanotubes:
  • 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.
  • Instructions: [html] [pdf, 435k]
  • Required tutorial files: [.tar.gz, 39.8M], [.zip, 39.8M], [individual files]




Modeling Nanopores for Sequencing DNA
Modeling Nanopores for Sequencing DNA:
  • 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.
  • Instructions: [pdf, 15M]
  • Required tutorial files: [.tar.gz, 277M]


Specialized Topics

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
Parameterizing a Novel Residue:
  • 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.
  • Instructions: [html] [pdf, 2.5M]
  • Required tutorial files (all versions): [.tar.gz, 24.2M], [.zip, 24.2M], [individual files (all versions)]




Topology File Tutorial
Topology File Tutorial:
  • 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.
  • Instructions: [html] [pdf, 4.4M]
  • Required tutorial files: [.tar.gz, 11.2M], [.zip, 11.2M], [individual files]




Membrane Proteins Tutorial
Membrane Proteins Tutorial:
  • 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.
  • Instructions: [pdf, 1.0M]
  • Required tutorial files: reduced version [.tar.gz, 10.2M]; full version, [.tar.gz, 508M]




Residue-Based Coarse-Graining
Residue-Based Coarse-Graining:
  • The tutorial reviews residue-based coarse-graining, a method in which several atoms of a biological macromolecule are grouped together in a “virtual” bead (e.g., a single amino acid is represented by 2-5 beads). The reduction in degrees of freedom makes the model computationally efficient alternative to atomistic models, allowing for simulations to be run on larger systems and longer time scales. Requires VMD, "Nightly Build" of NAMD (Linux only) or NAMD 2.10 (when available) to complete the tutorial. Tutorial works on Linux only.
  • Instructions: [pdf, 1.5M]
  • Required tutorial files: [.tar.gz, 124M]




Shape-Based Coarse Graining
Shape-Based Coarse Graining:
  • 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.
  • Instructions: [html] [pdf, 2.4M]
  • Required tutorial files: [.zip, 6.5M], [individual files]




Molecular Dynamics Flexible Fitting (MDFF)
Molecular Dynamics Flexible Fitting (MDFF):
  • 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.
  • Instructions: [html] [pdf, 1.3M]
  • Required tutorial files: [.tar.gz, 98.2M] [.zip, 98.2M], [individual files]




Timeline Tutorial
Timeline: a VMD Plugin for Trajectory Analysis:
  • 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. Requires VMD.
  • Instructions: [html] [pdf, 2.5M]
  • Required tutorial files: [.tar.gz, 58.0M] [.zip, 58.0M], [individual files]




Molefacture Tutorial
Molefacture: A Tutorial to Build and Edit Molecules:
  • Molefacture is a VMD plugin that has been designed to facilitate the construction and parameterisation of small molecules. It additionally provides a simple interface to prepare structures and files for free energy perturbation calculations using NAMD. This tutorial serves as a primer for structure building, modification and parameterization using the molefacture plugin of VMD. Prior knowledge of NAMD and standard molecular dynamics simulations is assumed. Requires VMD, NAMD, and Amber.
  • Instructions: [pdf, 4.7M]
  • Required tutorial files: [.tar.gz, 17k] [.zip, 21k], [individual files]



Case Studies

In addition to the above tutorials, the Center provides case studies that utilize VMD to provide in-depth explorations of molecular systems. Topics examined in case studies include: water; DNA; lipid bilayers; BPTI; ubiquitin; myoglobin; aquaporin; ion channels; titin; and, light harvesting complex 2.

Additional Resources