title: Efficient Solvation Free Energy Calculations of Amino Acid Analogs by Expanded Ensemble Molecular Simulation.
abstract: We present an efficient, automated expanded ensemble method to calculate the residual chemical potential or solvation free energy by molecular dynamics simulation. The methodology is validated by computing the residual chemical potential of 13 amino acid analogs in water at 300 K and 1 bar and comparing to reference simulation data. Overall agreement is good, with the methodology of the present study reaching limiting precisions of less than 0.1 kBT in half of the total simulation time of the reference simulation study which utilized Bennett's acceptance ratio method. The apparent difference in the efficiencies is a result of the inherent advantages of the expanded ensemble method, which creates an improved decorrelation of simulation data and improves the sampling of the important regions of the configurational phase space of each subensemble. The present adaptation utilizes histograms of proposed transition energies collected throughout the entire simulation, to make extremely precise calculations of the relative free energy between neighboring subensembles.
authors.affiliation: Department of Chemical and Biomolecular Engineering and ‡Center for Research Computing, University of Notre Dame , Notre Dame, Indiana 46556, United States.
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Paluch
authors.affiliation: Department of Chemical and Biomolecular Engineering and ‡Center for Research Computing, University of Notre Dame , Notre Dame, Indiana 46556, United States.
authors.forename: Jindal K
authors.initials: JK
authors.lastname: Shah
authors.affiliation: Department of Chemical and Biomolecular Engineering and ‡Center for Research Computing, University of Notre Dame , Notre Dame, Indiana 46556, United States.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Maginn