A Simple Method for Automated Equilibration Detection in Molecular Simulations

Journal of Chemical Theory and Computation
John Damon Chodera

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.

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Citations

May 16, 2018·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Andreas SingraberChristoph Dellago
Dec 11, 2019·Journal of Computational Chemistry·William M MenzerDavid D L Minh
Jun 21, 2019·Nature Communications·Gerard MinuesaMichael G Kharas
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Jul 28, 2018·Science·Sandro Bottaro, Kresten Lindorff-Larsen
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Jan 23, 2021·The Journal of Chemical Physics·Kevin S Silmore, James W Swan
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