Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space
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.
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Journal
The Journal of Chemical PhysicsVolume
136Number
164103Issue
16Start page
1End page
17Total pages
17Publisher
American Institute of PhysicsPlace published
United StatesLanguage
EnglishCopyright
© 2012 American Institute of PhysicsFormer Identifier
2006029004Esploro creation date
2020-06-22Fedora creation date
2012-07-09Usage metrics
Keywords
Acceptance ratioAsymmetric modelsBennett acceptance ratioBiased samplingBiological mechanismsBrownian DynamicsConfigurational spacesElectrostatic contributionsEnergy differencesExcess chemical potentialsExperimental dataFree energy perturbationFree-energy calculationsFree-energy differenceHarmonic oscillatorsHistogram analysisIon channelIon selectivityLeast SquareMarginalizationNon-equilibrium processPopulation densitiesReaction coordinatesRelative binding affinitySolvation free energiesStringent testTwo-stateUmbrella samplingUniform sampling
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