IPython Notebook Tutorials

These IPython (http://ipython.org) notebooks show the usage of the PyEMMA API in action and also describe the workflow of Markov model building.

MSM estimation and validation

• MSM Estimation
  • IO
  • Trajectory generation
  • Estimation
  • Implied timescales
  • Example: Double-well potential
• MSM-analysis for alanine-dipeptide
  • Use ipythons magic % commands to activate plotting within notebook cells
  • Imports are ordered as
  • Load necessary input data
  • Eigenvectors
  • Eigenvalues
  • Implied time scales
  • PCCA
  • Summary
• Implied timescales notebook
  • Helper functions
  • Example: Double-well potential
  • Test
• Fingerprint analysis for alanine-dipeptide
  • Use ipythons magic % commands to activate plotting within notebook cells
  • Imports are ordered as
  • Load necessary input data
  • Metastable sets
  • Observables
  • Initial distribution
  • Fingerprint relaxation
• Transition path analysis for alanine-dipeptide
  • Metastable sets
  • Easy computation of transition paths between sets