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

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

OpenMM: A Hardware-Independent Framework for Molecular Simulations

(2010) Peter Eastman et al.   COMPUTING IN SCIENCE & ENGINEERING

Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations

(2010) Peter Eastman et al.   Journal of Chemical Theory and Computation

Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages

(2009) David D. L. Minh et al.   JOURNAL OF CHEMICAL PHYSICS

Error and efficiency of replica exchange molecular dynamics simulations

(2009) Edina Rosta et al.   JOURNAL OF CHEMICAL PHYSICS

Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations

(2009) Edina Rosta et al.   Journal of Chemical Theory and Computation

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Strengths and weaknesses of parallel tempering

(2009) J. Machta   PHYSICAL REVIEW E

What Makes Molecular Dynamics Work?

(2009) Robert D. Skeel   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics

(2008) Ben Cooke et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Exchange frequency in replica exchange molecular dynamics

(2008) Daniel Sindhikara et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptide folding kinetics from replica exchange molecular dynamics

(2008) Nicolae-Viorel Buchete et al.   PHYSICAL REVIEW E