title: A Simple Method for Automated Equilibration Detection in Molecular Simulations.
abstract: Molecular simulations intended to compute equilibrium properties are often initiated from configurations that are highly atypical of equilibrium samples, a practice which can generate a distinct initial transient in mechanical observables computed from the simulation trajectory. Traditional practice in simulation data analysis recommends this initial portion be discarded to equilibration, but no simple, general, and automated procedure for this process exists. Here, we suggest a conceptually simple automated procedure that does not make strict assumptions about the distribution of the observable of interest in which the equilibration time is chosen to maximize the number of effectively uncorrelated samples in the production timespan used to compute equilibrium averages. We present a simple Python reference implementation of this procedure and demonstrate its utility on typical molecular simulation data.
authors.affiliation: Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , 1275 York Avenue, Box 357, New York, New York 10065, United States.
authors.forename: John D
authors.initials: JD
authors.lastname: Chodera
mesh_terms: D000465:Algorithms; D008390:Markov Chains; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method