title: Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets.
abstract: We extend the theory of hybrid explicit/implicit solvent models to include an explicit domain that grows and shrinks in response to a solute's evolving configuration. The goal of this model is to provide an appropriate but not excessive amount of solvent detail, and the inclusion of an adjustable boundary provides a significant computational advantage for solutes that explore a range of configurations. In addition to the theoretical development, a successful implementation of this method requires (1) an efficient moveset that propagates the boundary as a new coordinate of the system, and (2) an accurate continuum solvent model with parameters that are transferable to an explicit domain of any size. We address these challenges and develop boundary updates using Monte Carlo moves biased by nonequilibrium paths. We obtain the desired level of accuracy using a "decoupling interface" that we have previously shown to remove boundary artifacts common to hybrid solvent models. Using an uncharged, coarse-grained solvent model, we then study the efficiency of nonequilibrium paths that a simulation takes by quantifying the dissipation. In the spirit of optimization, we study this quantity over a range of simulation parameters.
authors.affiliation: Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA.
authors.forename: Jason A
authors.initials: JA
authors.lastname: Wagoner
authors.affiliation: Department of Chemistry, Department of Structural Biology, and Department of Computer Science, Stanford University, Stanford, California 94305-5080, USA.
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
mesh_terms: D003198:Computer Simulation; D009010:Monte Carlo Method; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry
chemical_list: D012997:Solvents; D014867:Water