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TCBG Summer School - Urbana, Jun. 2-13, 2003

Tutorials

• Mon, 6/2: Introduction to Protein Structure and Dynamics
  • Molecular Graphics Tutorial  - An introduction to VMD and its capabilities
    
    
• Tue, 6/3: Statistical Mechanics of Proteins
  • Molecular Dynamics Tutorial  - An introduction to NAMD and its capabilities
    
    
• Wed, 6/4: Steered Molecular Dynamics of Proteins
  • Stretching Deca-Alanine Tutorial - An introduction to IMD and SMD simulations with VMD and NAMD
    
    
• Thu, 6/5: Simulating Membrane Channels
  • Water Channel Tutorial - A tutorial simulating water diffusion and permeation through nanotubes
    
    
• Fri, 6/6: Quantum Chemistry of Proteins
  • Introduction to Quantum Mechanics Simulations (html) (pdf, 316K) - An introduction to quantum mechanical (QM) simulation
    
    • input files (.tar.gz, 1.6M)
  
  
• Mon, 6/9: Parameters for Classical Force Fields
  • Determining Force Fields  - Tutorial on determining new force field parameters to describe novel system components of a new molecule
    
    
• Tue, 6/10: Bioinformatics of Proteins
  • Bioinformatics - Tutorial on using Bioinformatics to classify protein domains and align determined protein domains structurally
    
    
• Wed, 6/11: Simulation of Lipids; Parallel Computing
  • Parallel Computing (pdf, 116K) - Tutorial on Parallelizing MD Simulations
    • charm input files (.tgz, 3.3M)
    • logs input files (.tgz, 9.8M)
    • NAMD2 input files (.tgz, 1.1M)
  
  
• Thu, 6/12: Numerical Algorithms
  • Numerical Laboratory (pdf, 82K) - A tutorial on numerical algorithms
    
  • Cluster Building Tutorial (html) - Tutorial on building your own computer cluster
  
  
• Fri, 6/13: Modeling Large Systems
  • Excitation and Electron Transfer (html) (pdf, 794K)
    • input files (.tar.gz, 3.5M)