I’m trying to learn Markov state models for my MD analysis. I will put thoughts and notes here.
- There are 2 popular Python modules, PyEMMA and MSMbuilder. I’m sticking to PyEMMA at the moment because I had trouble installing the other
- Intro to MSM by Frank Noé 1h+, volume is a bit low
- MSM for Simulation Analysis by Kyle Beauchamp ~20m
- PyEMMA Jupyter notebook tutorials
- Usually my eyes glaze over at statistical mechanics maths, but the PyEMMA paper is surprisingly very readable and easy to follow