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Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures

Please always quote using this URN:urn:nbn:de:0296-matheon-10998
  • Dynamical averages based on functionals of dynamical trajectories, such as time-correlation func- tions, 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 prop- erties 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 of 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 us- ing 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.

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Metadaten
Author:John D. Chodera, William C. Swope, Frank Noe, Jan-Hendrik Prinz, Michael R. Shirts, Vijay S. Pande
URN:urn:nbn:de:0296-matheon-10998
Referee:Christof Schütte
Document Type:Preprint, Research Center Matheon
Language:English
Date of first Publication:2012/02/27
Release Date:2012/02/27
Tag:Weighted histogram analysis method (WHAM); extended bridge sampling (EBS); molecular dynamics; multiple histogram reweighting; multistate Bennett acceptance ratio (MBAR); parallel tempering; temperature reweighting; temperature-dependent dynamics
Institute:Research Center Matheon
Freie Universität Berlin
MSC-Classification:62-XX STATISTICS / 62Mxx Inference from stochastic processes / 62M05 Markov processes: estimation
Preprint Number:941
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