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.

  • 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. Requires VMD.

  • Molefacture: A Tutorial to Build and Edit Molecules (pdf, 4.7M) (required tutorial files [.tar.gz, 17k] [.zip, 21k], individual files)
    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.

  • Residue-Based Coarse-Graining (pdf, 1.5M) (required tutorial files [.tar.gz, 124M] )
    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.

  • PHI: Open Quantum Dynamics of Multi-Molecule Systems (pdf, 531K) (required tutorial files, [.tar.gz, 186 KB])
    The tutorial provides some basic examples to explain how to calculate the dynamics of a quantum system in contact with a thermal environment using the hierarchy equations of motion integration software PHI. Requires the PHI software, as found here. Linux only.

  • 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.

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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