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Online Workshop

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.

Supplemental Tutorials

• The workshop assumes working familiarity with VMD and NAMD. The supplemental tutorials below may help you learn both softwares if you need greater familiarity with the tools.


• Using VMD (html) (pdf, 16.3M) (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.
  
  
• 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.

Tutorial Assistance

• Workshop participants may contact teaching assistants about the Membrane Proteins or Nanotubes tutorials by writing memprot-workshop@ks.uiuc.edu.