1.9k citations · 3.3k across the 21 of their papers we have counts for
10 papers · 1 filter
Replica exchange of expanded ensembles: A generalized ensemble approach with enhanced flexibility and parallelizability
Wei-Tse Hsu, Michael R. Shirts
Generalized ensemble methods such as Hamiltonian replica exchange (HREX) and expanded ensemble (EE) have been shown effective in free energy calculations for various contexts, give…
Adding alchemical variables to metadynamics to enhance sampling in free energy calculations
Wei-Tse Hsu, Valerio Piomponi, Pascal T. Merz +2
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculation…
How cooperatively folding are homopolymer molecular knots?
Christopher C. Walker, Theodore L. Fobe, Michael R. Shirts
Detailed thermodynamic analysis of complex systems with multiple stable configurational states allows for insight into the cooperativity of each individual transition. In this work…
Enhanced sampling methods for molecular dynamics simulations
Jérôme Hénin, Tony Lelièvre, Michael R. Shirts +2
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration…
Statistically optimal continuous free energy surfaces from biased simulations and multistate reweighting
Michael R. Shirts, Andrew L. Ferguson
Free energies as a function of a selected set of collective variables are commonly computed in molecular simulation and of significant value in understanding and engineering molecu…
Configurational mapping significantly increases the efficiency of solid-solid phase coexistence calculations via molecular dynamics: Determining the FCC-HCP coexistence line of Lennard-Jones particles
Natalie P. Schieber, Michael R. Shirts
In this study, we incorporate configuration mapping between simulation ensembles into the successive interpolation of multistate reweighting (SIMR) method in order to increase phas…
Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams
Natalie P. Schieber, Eric C. Dybeck, Michael R. Shirts
Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optic…
Reweighting from the mixture distribution as a better way to describe the Multistate Bennett Acceptance Ratio
Michael R. Shirts
The multistate Bennett Acceptance Ratio is provably the lowest variance unbiased estimator of both free energies and ensemble averages, and has a number of important advantages ove…
Simple quantitative tests to validate sampling from thermodynamic ensembles
Michael R. Shirts
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present…
Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
John D. Chodera, Michael R. Shirts
The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in e…