MSM analysis

End-to-end Markov-state-model analyses on real systems. Each tutorial walks the simulation-list → projection → clustering → model → kinetics pipeline from a set of trajectories to a model with timescales, free-energy surfaces, and rates.

Note

These tutorials download multi-GB trajectory sets from Figshare and run the full MSM pipeline. They take a long time and are intended to be executed locally - the docs build skips re-executing them, so the outputs you see here came from a prior local run.

• Protein folding MSM: villin headpiece
• Ligand binding MSM: trypsin + benzamidine