Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin

Sculpting bespoke mountains: Determining free energies with basis expansions

(2015) Jonathan K. Whitmer et al.   JOURNAL OF CHEMICAL PHYSICS

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

(2015) Alejandro Gil-Ley et al.   Journal of Chemical Theory and Computation

Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics

(2015) Jim Pfaendtner et al.   Journal of Chemical Theory and Computation

Well-Tempered Variational Approach to Enhanced Sampling

(2015) Omar Valsson et al.   Journal of Chemical Theory and Computation

Accelerated molecular dynamics simulations of protein folding

(2015) Yinglong Miao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering

(2015) Tong Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Variationally Optimized Free-Energy Flooding for Rate Calculation

(2015) James McCarty et al.   PHYSICAL REVIEW LETTERS

Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps

(2015) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Locating landmarks on high-dimensional free energy surfaces

(2015) Ming Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

On inference of causality for discrete state models in a multiscale context

(2014) S. Gerber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Applications of the Cross-Entropy Method to Importance Sampling and Optimal Control of Diffusions

(2014) Wei Zhang et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Molecular determinants of drug–receptor binding kinetics

(2013) Albert C. Pan et al.   DRUG DISCOVERY TODAY

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign

(2012) Petra Kührová et al.   BIOPHYSICAL JOURNAL

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

(2012) Michael Deighan et al.   Journal of Chemical Theory and Computation

Free energy computations by minimization of Kullback–Leibler divergence: An efficient adaptive biasing potential method for sparse representations

(2012) I. Bilionis et al.   JOURNAL OF COMPUTATIONAL PHYSICS

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Coarse-graining errors and numerical optimization using a relative entropy framework

(2011) Aviel Chaimovich et al.   JOURNAL OF CHEMICAL PHYSICS

Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations

(2011) Meher K. Prakash et al.   Journal of Chemical Theory and Computation

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Enhanced Sampling in the Well-Tempered Ensemble

(2010) M. Bonomi et al.   PHYSICAL REVIEW LETTERS

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

(2010) C. F. Abrams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A self-learning algorithm for biased molecular dynamics

(2010) Gareth A. Tribello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error and efficiency of replica exchange molecular dynamics simulations

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

Gaussian-Mixture Umbrella Sampling

(2009) Paul Maragakis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Crystal Structure of a Ten-Amino Acid Protein

(2008) Shinya Honda et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS