Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space

The Journal of Chemical Physics
Ilsoo Kim, Toby W Allen

Abstract

Free energy perturbation, a method for computing the free energy difference between two states, is often combined with non-Boltzmann biased sampling techniques in order to accelerate the convergence of free energy calculations. Here we present a new extension of the Bennett acceptance ratio (BAR) method by combining it with umbrella sampling (US) along a reaction coordinate in configurational space. In this approach, which we call Bennett acceptance ratio with umbrella sampling (BAR-US), the conditional histogram of energy difference (a mapping of the 3N-dimensional configurational space via a reaction coordinate onto 1D energy difference space) is weighted for marginalization with the associated population density along a reaction coordinate computed by US. This procedure produces marginal histograms of energy difference, from forward and backward simulations, with higher overlap in energy difference space, rendering free energy difference estimations using BAR statistically more reliable. In addition to BAR-US, two histogram analysis methods, termed Bennett overlapping histograms with US (BOH-US) and Bennett-Hummer (linear) least square with US (BHLS-US), are employed as consistency and convergence checks for free energy diff...Continue Reading

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Citations

Jan 6, 2016·Journal of Chemical Theory and Computation·Xiangyu JiaYe Mei
Dec 31, 2015·The Journal of Physical Chemistry. B·Ilsoo Kim, Arieh Warshel
Aug 21, 2015·Biochimica Et Biophysica Acta·Ilsoo Kim, Arieh Warshel
Nov 20, 2016·Journal of Computational Chemistry·Ester SesmeroIan F Thorpe
May 31, 2017·Physical Chemistry Chemical Physics : PCCP·Zhao X SunJohn Z H Zhang
Feb 15, 2019·Journal of Computational Chemistry·Xiaohui WangZhaoxi Sun
Jun 22, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Yuan ChenJin-Gui Zheng
Jun 28, 2019·Chemical Reviews·Emelie FloodToby W Allen
May 16, 2018·The Journal of Physical Chemistry. C, Nanomaterials and Interfaces·Kevin R Hinkle, Frederick R Phelan
Jan 1, 2020·The Journal of Physical Chemistry. C, Nanomaterials and Interfaces·Kevin R Hinkle, Frederick R Phelan

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Software Mentioned

PERT
WHAM
BHLS
CFT
US
BAR
BOH
CHARMM

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