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Notebook tutorial

A runnable Jupyter notebook with rendered plots lives at examples/notebooks/adaptive_msm_tutorial.ipynb. It uses small synthetic examples so every figure renders in seconds without running molecular dynamics.

It covers, end to end:

  1. The input file — load the annotated template and validate it against the schema.
  2. VAMP-2 feature selection — rank candidate feature sets and pick the informative ones.
  3. MSM estimation — build an MSM from a synthetic metastable chain and plot implied timescales and metastable free energies.
  4. Convergence detection — watch the ConvergenceMonitor fire.
  5. Weighted-ensemble resampling — split/merge with conserved weight.
  6. The analysis report — synthesise a run directory and render the multi-panel plot_convergence_report.

Run it yourself

pip install -e ".[deep-tica,examples]" jupyter
jupyter notebook examples/notebooks/adaptive_msm_tutorial.ipynb

Then continue with a real campaign using the input file and the adaptive-MSM tutorial.