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Summer School Lectures

Lectures

All lectures of the Theoretical and Computational Biophysics Summer School are now available on video. The summer school tutorials have proven to be valuable for self-study of the practical use of VMD and NAMD. Now together with the lectures it becomes even easier to learn modeling using VMD, NAMD, and BioCoRE through the internet.

• 6/2: Introduction to Protein Structure and Dynamics (K. Schulten)
  • Welcome, Opening Remarks, and Overview (pdf, 8.5M) (Video)
  • Molecular Graphics Perspective of Protein Structure and Function (pdf, 4.3M) (Video)
  • Molecular Dynamics Methods (Part 1) (pdf, 3.0M) (Video)
  • Molecular Dynamics Methods (Part 2) (pdf, 3.2M) (Video)
  • Equilibrium Properties of Proteins (pdf, 5.6M) (Video)
  
  
• 6/3: Statistical Mechanics of Proteins (I. Kosztin)
  • Equilibrium and Nonequilibrium Properties of Proteins (pdf, 796K) (Video)
  • Coherent Motion in Proteins: Temperature Echoes (pdf, 134K) (Video)
  • Simulated Cooling of Proteins (pdf, 881K) (Video)
  
  
• 6/4: Steered Molecular Dynamics of Proteins (K. Schulten)
  • Introduction and Examples (pdf, 7.0M) (Video)
  • Mechanical Proteins (pdf, 9.5M) (Video)
  • Determining Potentials (pdf, 1.2M) (Video)
  
  
• 6/5: Simulating Membrane Channels (E. Tajkhorshid)
  • Introduction and Examples (pdf, 4.3M) (Video)
  • Transport in Aquaporins (pdf, 29M) (Video)
  • Nanotubes (pdf, 4.7M) (Video)
  
  
• 6/6: Quantum Chemistry of Proteins (T. Martinez)
  • Introduction and Examples (pdf, 6.8M) (Video)
  • Ab Initio and Semiempirical Quantum Chemistry (pdf, 3.5M) (Video)
  • QM/MM Methods and Direct Dynamics (pdf, 1.3M) (Video)
  
  
• 6/9: Parameters for Classical Force Fields (Z. Schulten)
  • Introduction and Examples (pdf, 1.3M) (Video)
  • Introduction to Classical Force Fields (pdf, 1.3M) (Video)
  • Methods of Parameterization (pdf, 1.7M) (Video)
  
  
• 6/10: Bioinformatics of Proteins (Z. Schulten)
  • Protein Structure Prediction and Function (pdf, 19M) (Video)
  • Sequence and Structure Alignment Algorithms (pdf, 19M) (Video)
  • Sequence and Structural Analysis Tools on the Web (pdf, 19M) (Video)
  
  
• 6/11: Simulation of Lipids (M. Klein); Parallel Computing (L. Kale)
  • Atomic Level Simulation of Membranes (pdf, 12M) (Video)
  • Coarse Grained Modeling of Lipid Phases (pdf, 12M) (Video)
  • Introduction to Parallel Computing Issues (pdf, 1.9M) (Video)
  • Cluster Building (pdf, 897K) (Video)
  
  
• 6/12: Numerical Algorithms (T. Schlick, R. Skeel)
  • Force Evaluation, Integrators, and Propagators (pdf, 473K) (Notes (pdf, 207K) ), (Slides (pdf, 473K)) (Video)
  • Optimization Techniques (pdf, 17M) (Homework 1: Biphenyl Minimization (pdf, 161K) ) (Video)
  • Monte Carlo Methods (pdf, 17M) (Homework 2: Global Optimization (pdf, 161K) ) (Video)
  
  
• 6/13: Modeling Large Systems (K. Schulten)
  • Molecular Machines of the Living Cell (pdf, 10M) (Video)
  • Light Harvesting in Photosynthesis (pdf, 24M) (Video)
  • ATP Synthase (pdf, 23M) (Video)