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Computational Biophysics Workshop - Champaign, Jul. 6-10, 2009

Day 1: Introduction to Protein Structure and Dynamics, K. Schulten

• Opening Remarks (pdf, 185K)
• Structure and Sequence Analysis with VMD (pdf,606K; pdf, 461K)
• VMD for Structure Building and Dynamics Analysis (pdf, 792K)

Day 2: Statistical Mechanics of Proteins, K. Schulten

• Molecular Dynamics with NAMD I (pdf,792K; pdf, 362K)
• Molecular Dynamics with NAMD II (pdf, 285K; pdf, 1.1M)

Day 3: Parameters for Classical Force Fields, E. Tajkhorshid

• Introduction to Topology, Parameters, and Structure Files (pdf, 1.1M)
• Examples and Applications (pdf, 1.1M)

Day 4: Simulating Membrane Channels, E. Tajkhorshid

• Introduction and Examples (pdf, 5.0M)
• Membrane Transporters; Nanotubes (pdf, 2.3M)

Day 5: Introduction to Bioinformatics, Z. Luthey-Schulten

• Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD
• Application of MultiSeq to Evolution of Translation Machinery