Workshop Tutorials

Workshop Tutorials
At each workshop, attendees spend the latter half of each day working on tutorials developed by the Resource. These tutorials provide "hands-on" experience with various software packages, most notably the Resource-produced  VMD and NAMD programs.  Below is a list of the tutorials, including the text of the tutorials in html and pdf format, and the files required for each tutorial.  Visitors to this site are encouraged to download the tutorials, work through them at their own pace. 

The tutorials each require one or more software packages to complete; account for the software requirements before attempting to proceed.  Where once written only for the Mac platform, current versions of the tutorials are written to work on Mac, Unix/Linux, and the Windows platform. A list of software requirements, and discussions of where to place the files used by a tutorial, are included at the start of each tutorial.
 
  • Aquaporins with the VMD MultiSeq Tool (html) (pdf, 1.9M) (required tutorial files [.tar.gz, 248M])
    A tutorial that uses Bioinformatics tools within VMD to find important structural features in aquaporins from evolutionary studies.
     
  • Evolution of Biomolecular Structure: Class II tRNA-Synthetases and tRNA (pdf, 3.0M) (required tutorial files [.tar.gz, 171M])
    A tutorial that uses structural and sequence alignment to learn about the evolution of tRNA synthetases.
     
  • NAMD Tutorial
    (html for Unix/Mac) (pdf for Unix/Mac, 8.0M)
    (html for Windows) (pdf for Windows, 6.5M)
    (required tutorial files (all platforms) [.tar.gz, 148M])
    An introduction to NAMD and its capabilities.
     
  • Parameterizing a Novel Residue (html) (pdf, 2.5M) (required tutorial files [.tar.gz, 24M])
    Tutorial on determining new force field parameters to describe novel system components of a new molecule.
     
  • Sequence Alignment Algorithms (pdf, 1.6M) (required tutorial files [.tar.gz, 570K])
     
  • Simulation of Water Permeation through Nanotubes (html) (pdf, 435K) (required tutorial files [.tar.gz, 40M])
    A tutorial simulating water diffusion and permeation through nanotubes.
     
  • Stretching Deca-Alanine (html) (pdf, 1.4M) (required tutorial files [.tar.gz, 5.3M])
    An introduction to IMD and SMD simulations with VMD and NAMD.
     
  • Topology File Tutorial (html) (pdf, 4.4M ) (required tutorial files [.tar.gz, 11M])
    An introduction on how to generate parameter information for a molecule based on topology information from other molecules.
     
  • VMD Molecular Graphics (html) (pdf, 18M) (required tutorial files [.tar.gz, 45M])
    An introduction to VMD and its capabilities.
     

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