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A robust approach to estimating rates from time-correlation functions
John D. Chodera, Phillip J. Elms, William C. Swope +5
While seemingly straightforward in principle, the reliable estimation of rate constants is seldom easy in practice. Numerous issues, such as the complication of poor reaction coord…
Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations
David A. Sivak, John D. Chodera, Gavin E. Crooks
Common algorithms for computationally simulating Langevin dynamics must discretize the stochastic differential equations of motion. These resulting finite time step integrators nec…
Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
John D. Chodera, Michael R. Shirts
The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in e…
Nonequilibrium candidate Monte Carlo: A new tool for efficient equilibrium simulation
Jerome P. Nilmeier, Gavin E. Crooks, David D. L. Minh +1
Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte…
Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments
John D. Chodera, Vijay S. Pande
To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along wh…
Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes: theory and application to free energies, moments, and thermodynamic length in single-molecule pulling experiments
David D. L. Minh, John D. Chodera
Recently discovered identities in statistical mechanics have enabled the calculation of equilibrium ensemble averages from realizations of driven nonequilibrium processes, includin…
Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages
David D. L. Minh, John D. Chodera
Existing optimal estimators of nonequilibrium path-ensemble averages are shown to fall within the framework of extended bridge sampling. Using this framework, we derive a general m…