Tutorials

To complete the tutorials, you will need 1) a copy of the tutorial texts, as available in html and pdf forms below, 2) the files required to complete the tutorials (download all in a compressed file or individually as provided below), and 3) appropriate software as detailed in each tutorial, including VMD and NAMD. See also the workshop technical requirements page.

Simulating Membrane Channels Tutorials

  • Membrane Proteins Tutorial (pdf, 4.5M) (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.

  • Simulation of Water Permeation through Nanotubes (html) (pdf, 381k) (required tutorial files [.tar.gz, 39.8M], individual files)
    Investigates the permeation of water through nanotubes, as a model for transmembrane permeation of substrates through channels. Requires VMD 1.8.4 or higher, a current version of NAMD, and a text editor. Tutorial works on Windows, Mac, and Unix/Linux platforms.

Preparatory Tutorials (to be completed if you are not already familiar with VMD and NAMD)

Tutorial Assistance