Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics.

Markovian state models (MSMs) are a convenient and efficient means to compactly describe the kinetics of a molecular system as well as a formalism for using many short simulations to predict long time scale behavior. Building a MSM consists of grouping the conformations into states and estimating the transition probabilities between these states. In a previous paper, we described an efficient method for calculating the uncertainty due to finite sampling in the mean first passage time between two states.