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

John D. Chodera, William C. Swope, Frank Noé, Jan-Hendrik Prinz, Michael R. Shirts, and Vijay S. Pande.
J. Chem. Phys. 134:244107, 2011. [DOI] [PDF

We describe how reweighing techniques can provide optimal estimates of temperature-dependent dynamical properties from simulations conducted at multiple temperatures.

Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes

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 and John D. Chodera
J. Chem. Phys. 134:024111, 2011. [DOI] [PDF]

We derive a new estimator for estimating equilibrium expectations from nonequilibrium experiments, and show how it can be used to estimate a variety of useful quantities in simulated single-molecule force spectroscopy experiments.

Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution

John D. Chodera and Frank Noé.
J. Chem. Phys. 133:105102, 2010. [DOI] [PDF]

A simple Bayesian approach for the modeling of statistical uncertainties in kinetic and equilibrium quantities computed from Markov state models of biomolecular dynamics.

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

Sergio Bacallado, John D. Chodera, and Vijay S. Pande.
J. Chem. Phys. 131:045106, 2009. [DOI] [PDF

A Bayesian scheme for comparing state space decompositions for Markov state models of biomolecular dynamics that incorporates the fact that physical systems must obey detailed balance.  This paper utilizes recent results from Markov chain theory on edge-reinforced random walks.

Statistically optimal analysis of samples from multiple equilibrium states

Michael R. Shirts and John D. Chodera.  
J. Chem. Phys. 129:124105, 2008. [DOI] [PDF]

We present a highly general, statistically optimal approach for producing estimates of free energies and equilibrium expectations from multiple simulations that provably extracts all useful information from the data.

Keywords: Multistate Bennett acceptance ratio; MBAR; Bennett acceptance ratio; BAR; molecular dynamics; Monte Carlo; replica exchange