Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Efficient molecular dynamics using geodesic integration and solvent–solute splitting

(2016) Benedict Leimkuhler et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

The computation of averages from equilibrium and nonequilibrium Langevin molecular dynamics

(2015) Benedict Leimkuhler et al.   IMA JOURNAL OF NUMERICAL ANALYSIS

Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids

(2015) Debdas Dhabal et al.   JOURNAL OF CHEMICAL PHYSICS

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

(2015) Chad W. Hopkins et al.   Journal of Chemical Theory and Computation

Extra Chance Generalized Hybrid Monte Carlo

(2015) Cédric M. Campos et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems

(2014) David A. Sivak et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Robust and efficient configurational molecular sampling via Langevin dynamics

(2013) Benedict Leimkuhler et al.   JOURNAL OF CHEMICAL PHYSICS

Using Nonequilibrium Fluctuation Theorems to Understand and Correct Errors in Equilibrium and Nonequilibrium Simulations of Discrete Langevin Dynamics

(2013) David A. Sivak et al.   Physical Review X

Reducing the effect of Metropolization on mixing times in molecular dynamics simulations

(2012) Jason A. Wagoner et al.   JOURNAL OF CHEMICAL PHYSICS

Near-Equilibrium Measurements of Nonequilibrium Free Energy

(2012) David A. Sivak et al.   PHYSICAL REVIEW LETTERS

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

(2011) J. P. Nilmeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Free energy reconstruction from steered dynamics without post-processing

(2010) Manuel Athènes et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Implicit Mass-matrix Penalization of Hamiltonian Dynamics with Application to Exact Sampling of Stiff Systems

(2010) Petr Plecháč et al.   MULTISCALE MODELING & SIMULATION

Comment on “On the Crooks fluctuation theorem and the Jarzynski equality” [J. Chem. Phys. 129, 091101 (2008)]

(2009) Artur B. Adib   JOURNAL OF CHEMICAL PHYSICS

A separable shadow Hamiltonian hybrid Monte Carlo method

(2009) Christopher R. Sweet et al.   JOURNAL OF CHEMICAL PHYSICS

Erratum to “A comparison of generalized hybrid Monte Carlo methods with and without momentum flip” [J. Comput. Phys. 228 (2009) 2256–2265]

(2009) Elena Akhmatskaya et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Measurement of nonequilibrium entropy from space-time thermodynamic integration

(2008) Manuel Athènes 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