Episodes

List of course episodes:

Part I: Generating the data (OpenMM workflows)

  1. Episode 1: Introduction (environment and data)
  2. Episode 2: Running simulations
  3. Episode 3: Preparing and editing the system
  4. Episode 4: Advanced sampling and simulated annealing

Part II: Analyzing the results

  1. Episode 5: Trajectory analysis with MDTraj
  2. Episode 6: MSMs with PyEMMA
  3. Episode 7: MSMs with deeptime

Associated notebooks: docs/episodes/notebooks/. Associated scripts: docs/episodes/scripts/.