Abstract:Markov state models (MSMs) have become one of the preferred methods for the analysis and interpretation of molecular dynamics (MD)
simulations of conformational transitions in biopolymers. While there is great variation in terms of implementation, a well-defined
workflow involving multiple steps is often adopted. Typically, molecular coordinates are first subjected to dimensionality reduction and then clustered into small ``microstates'', which are subsequently lumped into ``macrostates'' using the informati… Show more
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