title: Density-dependent analysis of nonequilibrium paths improves free energy estimates.
abstract: When a system is driven out of equilibrium by a time-dependent protocol that modifies the Hamiltonian, it follows a nonequilibrium path. Samples of these paths can be used in nonequilibrium work theorems to estimate equilibrium quantities such as free energy differences. Here, we consider analyzing paths generated with one protocol using another one. It is posited that analysis protocols which minimize the lag, the difference between the nonequilibrium and the instantaneous equilibrium densities, will reduce the dissipation of reprocessed trajectories and lead to better free energy estimates. Indeed, when minimal lag analysis protocols based on exactly soluble propagators or relative entropies are applied to several test cases, substantial gains in the accuracy and precision of estimated free energy differences are observed.
authors.affiliation: Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, USA. daveminh@gmail.com
authors.forename: David D L
authors.initials: DD
authors.lastname: Minh
mesh_terms: D000465:Algorithms; D019411:Clinical Laboratory Techniques; D003198:Computer Simulation; D019277:Entropy; D008956:Models, Chemical; D055585:Physical Phenomena; D011487:Protein Conformation; D012107:Research Design; D013816:Thermodynamics