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

John D. Chodera and Michael R. Shirts.
J. Chem. Phys. 135:194110, 2011. [DOI] [PDF] 

We show how a simple change to the way exchanges are handled in the popular replica-exchange simulation methodology can enormously increase efficiency at no increase in computational cost.

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

Jan-Hendrik Prinz, John D. Chodera, Vijay S. Pande, Jeremy C. Smith, and Frank Noé.
J. Chem. Phys. 134:244108, 2011. [DOI] [PDF]