Methods Mol Biol. 2014;1084:141-58. doi: 10.1007/978-1-62703-658-0_8.
ABSTRACT
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.
PMID:24061920 | DOI:10.1007/978-1-62703-658-0_8