Lectures

  • 2/11: Introduction to Protein Structure and Dynamics - Klaus Schulten
    • Opening Remarks (pdf)
    • Structure and Sequence Analysis with VMD (pdf)
    • Introduction to Molecular Dynamics with NAMD (pdf)

  • 2/12: Statistical Mechanics of Proteins - Klaus Schulten
    • Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD (pdf)
    • Exemplary Applications of VMD / NAMD in Modern Research (pdf, pdf)

  • 2/13: Parameters for Classical Force Fields - Emad Tajkhorshid, Christopher Mayne
    • Introduction to Topology, Parameters, and Structure Files (pdf) - Tajkhorshid
    • Examples and Applications (pdf) - Tajkhorshid
    • A Brief Overview of the Force Field Toolkit (ffTK) (pdf, pdf) - Mayne

  • 2/14: Simulating Membrane Channels - Emad Tajkhorshid
    • Introduction and Examples (pdf)
    • Transport in Aquaporins; Nanotubes (pdf)

  • 2/15: Introduction to Bioinformatics - Zan Luthey-Schulten
    • Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD (pdf, pdf) (audio lecture)
    • Application of MultiSeq to Evolution of Translation Machinery (pdf)