Efficient estimation of free energy differences from Monte Carlo data

By Charles H. Bennett. 1976

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Citations in the corpus

Equivariant Flows: exact likelihood generative learning for symmetric densities (2020, methodology): “…to speed up rare events by adding a suitable bias energy to u(x) and subsequently correcting the generated distribution by reweighing or Monte-Carlo estimators using the ratio of true over generated density, e.g. (Torrie & Valleau, 1977; Bennett, 1976; Laio & Parrinello, 2002; Wu et al., 2016).”
Discrete Variational Autoencoders (2016, methodology): “For this purpose, we estimate the log partition function using bridge sampling, a variant of Bennett’s acceptance ratio method (Bennett, 1976; Shirts & Chodera, 2008), which produces unbiased estimates of the partition function.”
AmberTools (2023, unknown): “The edgembar program performs analysis of alchemical free energy simulations using the multistate Bennett acceptance ratio (MBAR) method, 57 the Bennett acceptance ratio (BAR) method, 58 exponential averaging, 59 thermodynamic integration, 60 or combinations of these approaches.”
Training Restricted Boltzmann Machines (2015, methodology): “Therefore, we explore ([8], Chapter 9) alternative techniques from statistical physics for estimating the normalization constant, including Bennetts Acceptance Ratio (BAR) [2].”
Training restricted Boltzmann machines: An introduction (2014, methodology): “As we will see later, a certain choice of P and P̃ leads to the estimator introduced by Bennett (1976) and generalized by Crooks (2000) and Shirts et al.”
Statistical Mechanics: Entropy, Order Parameters, and Complexity (2021, unknown): “densely (Definition 1), then there is ‘no more room’ for a second ergodic component with non-zero volume (Definition 2).(14) Conversely, if there (14)Mathematicians must be careful in the definitions and proofs to exclude different invariant sets that are infinitely finely intertwined.”
Guidelines for the analysis of free energy calculations (2015, methodology): “Some of them, like BAR [1] and MBAR [35], are in common use and are deeply entrenched in the parlance of the field, while others either do not have customary, generally accepted names, or remain little-known.”