# MSM analysis

End-to-end Markov-state-model analyses on real systems. Each tutorial walks the {doc}`simulation-list → projection → clustering → model → kinetics pipeline <../../explanation/msm-workflow>` 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](https://doi.org/10.6084/m9.figshare.32541291) 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.
```

```{toctree}
:maxdepth: 1

villin-folding
trypsin-benzamidine-binding
```