title: Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.
abstract: Dynamical averages based on functionals of dynamical trajectories, such as time-correlation functions, play an important role in determining kinetic or transport properties of matter. At temperatures of interest, the expectations of these quantities are often dominated by contributions from rare events, making the precise calculation of these quantities by molecular dynamics simulation difficult. Here, we present a reweighting method for combining simulations from multiple temperatures (or from simulated or parallel tempering simulations) to compute an optimal estimate of the dynamical properties at the temperature of interest without the need to invoke an approximate kinetic model (such as the Arrhenius law). Continuous and differentiable estimates of these expectations at any temperature in the sampled range can also be computed, along with an assessment of the associated statistical uncertainty. For rare events, aggregating data from multiple temperatures can produce an estimate with the desired precision at greatly reduced computational cost compared with simulations conducted at a single temperature. Here, we describe use of the method for the canonical (NVT) ensemble using four common models of dynamics (canonical distribution of Hamiltonian trajectories, Andersen thermostatting, Langevin, and overdamped Langevin or Brownian dynamics), but it can be applied to any thermodynamic ensemble provided the ratio of path probabilities at different temperatures can be computed. To illustrate the method, we compute a time-correlation function for solvated terminally-blocked alanine peptide across a range of temperatures using trajectories harvested using a modified parallel tempering protocol.
authors: California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA. jchodera@berkeley.edu
authors: John D
authors: JD
authors: Chodera
authors: William C
authors: WC
authors: Swope
authors: Frank
authors: F
authors: Noé
authors: Jan-Hendrik
authors: JH
authors: Prinz
authors: Michael R
authors: MR
authors: Shirts
authors: Vijay S
authors: VS
authors: Pande
mesh_terms: D000409:Alanine / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D013696:Temperature
chemical_list: D010455:Peptides; D000409:Alanine