Part of understanding a molecule’s conformational dynamics is mapping out the dominant metastable, or long lived, states that it occupies. Once identified, the rates for transitioning between these states may then be determined in order to create a complete model of the system’s conformational dynamics. Here we describe the use of the MSMBuilder package (now available at https://simtk.org/home/msmbuilder/) to build Markov State Models (MSMs) to identify the metastable states from Generalized Ensemble (GE) simulations, as well as other simulation datasets. Besides building MSMs, the code also includes tools for model evaluation and visualization.

Markov state models provide a framework for understanding the fundamental states and rates in the conformational dynamics of biomolecules. We describe an improved protocol for constructing Markov state models from molecular dynamics simulations. The new protocol includes advances in clustering, data preparation, and model estimation; these improvements lead to significant increases in model accuracy, as assessed by the ability to recapitulate equilibrium and kinetic properties of reference systems. A high-performance implementation of this protocol, provided in MSMBuilder2, is validated on dynamics ranging from picoseconds to milliseconds.

Markov state models MSMs are a powerful tool for modeling both the thermodynamics and kinetics of molecular systems. In addition, they provide a rigorous means to combine information from multiple sources into a single model and to direct future simulations/experiments to minimize uncertainties in the model. However, constructing MSMs is challenging because doing so requires decomposing the extremely high dimensional and rugged free energy landscape of a molecular system into long-lived states, also called metastable states. Thus, their application has generally required significant chemical intuition and hand-tuning. To address this limitation we have developed a toolkit for automating the construction of MSMs called MSMBUILDER available at https://simtk.org/home/msmbuilder. In this work we demonstrate the application of MSMBUILDER to the villin headpiece HP-35 NleNle, one of the smallest and fastest folding proteins. We show that the resulting MSM captures both the thermodynamics and kinetics of the original molecular dynamics of the system. As a first step toward experimental validation of our methodology we show that our model provides accurate structure prediction and that the longest timescale events correspond to folding.