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Computational Biophysics Workshop

Below is a list of the tutorials used at the workshop.   Please click here to see a page with the updated versions of these tutorials.


• VMD Molecular Graphics Tutorial
  An introduction to VMD and its capabilities.
  
  
• NAMD Molecular Dynamics/Steered Molecular Dynamics Tutorial
  An introduction to NAMD and its capabilities.
  
  
• Evolution of Protein: Aspartyl-tRNA Synthetase
  A tutorial that uses structural and sequence alignment to learn about the evolution of tRNA synthetases.
  
  
• Topology File Tutorial
  An introduction on how to generate parameter information for a molecule based on topology information from other molecules.
  
  
• Simuation of Water Permeation Through Nanotubes Tutorial
  A tutorial simulating water diffusion and permeation through nanotubes.
  
  
• Stretching Deca-Alanine Tutorial
  An introduction to IMD and SMD simulations with VMD and NAMD.
  
  
• Parameterization of a Novel Residue
  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.