ArticleThe Journal of chemical physics2011
Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.
Article in The Journal of chemical physics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- GOPAL: A Water Model with Improved Thermodynamic Properties over a Large Pressure and Temperature Range Optimized Using Multistate Reweighting and Configuration Space Mapping.Journal of chemical theory and computation · 2025Article
- Enhanced sampling without borders: on global biasing functions and how to reweight them.Physical chemistry chemical physics : PCCP · 2022Review
- Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective.Frontiers in molecular biosciences · 2022Review
- Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy.Journal of the American Chemical Society · 2021Article
- Molecular latent space simulators.Chemical science · 2020Article
- Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.Annual review of biophysics · 2019Review
- Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions.International journal of molecular sciences · 2018Article
- VAMPnets for deep learning of molecular kinetics.Nature communications · 2018Article
- Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium.Journal of chemical theory and computation · 2017Article
- Multiensemble Markov models of molecular thermodynamics and kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Pathways for virus assembly around nucleic acids.Journal of molecular biology · 2014Article
- Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins.Journal of chemical theory and computation · 2014Article
- Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems.The journal of physical chemistry. B · 2014Article
- Using Markov state models to study self-assembly.The Journal of chemical physics · 2014Article
- Markov state models of biomolecular conformational dynamics.Current opinion in structural biology · 2014Review
- The essential role of stacking adenines in a two-base-pair RNA kissing complex.Journal of the American Chemical Society · 2013Article
- A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations.Journal of chemical theory and computation · 2013Article
- The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein.Proteins · 2012Article
- Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.The Journal of chemical physics · 2011Article
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6 authors.
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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.
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