Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

Sufficient Conditions for Torpid Mixing of Parallel and Simulated Tempering

(2012) Dawn Woodard et al.   ELECTRONIC JOURNAL OF PROBABILITY

Measure-preserving integrators for molecular dynamics in the isothermal–isobaric ensemble derived from the Liouville operator

(2010) Tang-Qing Yu et al.   CHEMICAL PHYSICS

OpenMM: A Hardware-Independent Framework for Molecular Simulations

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

Generalized Replica Exchange Method

(2010) Jaegil Kim et al.   JOURNAL OF CHEMICAL PHYSICS

Error and efficiency of simulated tempering simulations

(2010) Edina Rosta et al.   JOURNAL OF CHEMICAL PHYSICS

Automated Sampling Assessment for Molecular Simulations Using the Effective Sample Size

(2010) Xin Zhang et al.   Journal of Chemical Theory and Computation

Optimal Weights in Serial Generalized-Ensemble Simulations

(2010) Riccardo Chelli   Journal of Chemical Theory and Computation

Exchange Often and Properly in Replica Exchange Molecular Dynamics

(2010) Daniel J. Sindhikara et al.   Journal of Chemical Theory and Computation

Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation Model

(2010) Yilin Meng et al.   Journal of Chemical Theory and Computation

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

(2010) Wei Jiang et al.   Journal of Chemical Theory and Computation

Conditions for rapid mixing of parallel and simulated tempering on multimodal distributions

(2009) Dawn B. Woodard et al.   ANNALS OF APPLIED PROBABILITY

Optimal temperature ladders in replica exchange simulations

(2009) Robert Denschlag et al.   CHEMICAL PHYSICS LETTERS

Efficiency of exchange schemes in replica exchange

(2009) Martin Lingenheil et al.   CHEMICAL PHYSICS LETTERS

Error and efficiency of replica exchange molecular dynamics simulations

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

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

(2009) Peter Eastman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accelerating molecular dynamic simulation on graphics processing units

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

Temperature random walk sampling of protein configurations

(2009) Ulrich H.E. Hansmann   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Phase transition in the three dimensional Heisenberg spin glass: Finite-size scaling analysis

(2009) L. A. Fernandez et al.   PHYSICAL REVIEW B

Strengths and weaknesses of parallel tempering

(2009) J. Machta   PHYSICAL REVIEW E

Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations

(2009) Daniel K. Shenfeld et al.   PHYSICAL REVIEW E

Rapid equilibrium sampling initiated from nonequilibrium data

(2009) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficiency reduction and pseudo-convergence in replica exchange sampling of peptide folding–unfolding equilibria

(2008) Robert Denschlag et al.   CHEMICAL PHYSICS LETTERS

Optimization of expanded ensemble methods

(2008) Fernando A. Escobedo et al.   JOURNAL OF CHEMICAL PHYSICS

Calculation of absolute protein-ligand binding free energy using distributed replica sampling

(2008) Tomas Rodinger 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

How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach

(2008) Hugh Nymeyer   Journal of Chemical Theory and Computation

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Comparison of the serial and parallel algorithms of generalized ensemble simulations: An analytical approach

(2008) Sanghyun Park   PHYSICAL REVIEW E

Asynchronous replica exchange for molecular simulations

(2007) Emilio Gallicchio et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY