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A set of uncorrelated configurations can be obtained from a correlated time series, such as is generated by a molecular dynamics or Metropolis Monte Carlo simulation, by subsampling the timeseries with an interval larger than the statistical inefficiency of the reduced potential uk of the timeseries. The statistical inefficiency can be estimated by standard procedures described in the following papers.
W. Janke, in Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms, edited by J. Grotendorst, D. Marx, and A. Murmatsu (John von Neumann Institute for Computing, J ̈ ulich, Germany, 2002), vol. 10, pp. 423–445
https://arxiv.org/abs/1704.00891
Elegant paper on how to derive MBAR using the idea of importance sampling from mixture distributions
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