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.

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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