TCB Hands-on Workshop in Urbana  



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