PT - JOURNAL ARTICLE AU - John D. Chodera TI - A simple method for automated equilibration detection in molecular simulations AID - 10.1101/021659 DP - 2015 Jan 01 TA - bioRxiv PG - 021659 4099 - http://biorxiv.org/content/early/2015/08/17/021659.short 4100 - http://biorxiv.org/content/early/2015/08/17/021659.full AB - 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.