title: Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics.
abstract: The performance and accuracy of different simulation schemes for estimating the entropy inferred from free energy calculations are tested. The results obtained from replica-exchange molecular dynamics (REMD) simulations based on a simplified toy model are compared to exact numerically derived ones to assess accuracy and convergence. It is observed that the error in entropy estimation decreases by at least an order of magnitude and the quantities of interest converge much faster when the simulations are coupled via a temperature REMD algorithm and the trajectories from different temperatures are combined. Simulations with the infinite-swapping method and its variants show some improvement over the traditional nearest-neighbor REMD algorithms, but they are more computationally expensive. To test the methodologies further, the free energy profile for the reversible association of two methane molecules in explicit water was calculated and decomposed into its entropic and enthalpic contributions. Finally, a strategy based on umbrella sampling computations carried out via simultaneous temperature and Hamiltonian REMD simulations is shown to yield the most accurate entropy estimation. The entropy profile between the two methane molecules displays the characteristic signature of a hydrophobic interaction.
authors.affiliation: Argonne Leadership Computing Facility, Argonne National Laboratory , 9700 South Cass Avenue, Building 240, Lemont, 60439 Illinois, United States.
authors.forename: Sunhwan
authors.initials: S
authors.lastname: Jo
authors.affiliation: Laboratoire International Associé Centre National de la Recherche Scientifique and University of Illinois at Urbana-Champaign, UMR 7565, Université de Lorraine , BP 70239, 54506 Vandœuvre-lès-Nancy, France.|Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.|Beckman Institute for Advanced Research and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews, Urbana, Illinois 61801, United States.
authors.forename: Christophe
authors.initials: C
authors.lastname: Chipot
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago , Chicago, Illinois 60637, United States.|Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Building 440, Argonne, Illinois 60439, United States.
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux
mesh_terms: D019277:Entropy; D008697:Methane / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D014867:Water / Q000737:chemistry
chemical_list: D014867:Water; D008697:Methane