A Tutorial on Building Markov State Models with MSMBuilder and Coarse-Graining Them with BACE

Markov state models (MSMs) are a powerful means of (1) making sense of molecular simulations, (2) making a quantitative connection between simulation and experiment, and (3) driving efficient simulations. A Markov model can be thought of as a map of the conformational space a molecule explores. Instead of having towns and cities connected with roads labeled with speed limits, a Markov model has conformational states and probabilities of transitioning between pairs of these states. This tutorial describes how to build Markov models and a few of the basic analyses that can be performed with the MSMBuilder software package.