Heating and flooding: A unified approach for rapid generation of free energy surfaces

Free Energy of Nascent-Chain Folding in the Translocon

(2011) James Gumbart et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Simplifying the representation of complex free-energy landscapes using sketch-map

(2011) Michele Ceriotti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhanced Sampling of Multidimensional Free-Energy Landscapes Using Adaptive Biasing Forces

(2011) Christophe Chipot et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin

(2010) Ludovico Sutto et al.   Journal of Chemical Theory and Computation

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

(2010) Pär Bjelkmar et al.   Journal of Chemical Theory and Computation

Free Energy Calculations: An Efficient Adaptive Biasing Potential Method

(2010) Bradley M. Dickson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Enhanced Conformational Sampling of Peptides via Reduced Side-Chain and Solvent Masses

(2010) I-Chun Lin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

(2009) Jérome Hénin et al.   Journal of Chemical Theory and Computation

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

(2009) Hernán Stamati et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Single-sweep methods for free energy calculations

(2008) Luca Maragliano et al.   JOURNAL OF CHEMICAL PHYSICS

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

Adaptively biased molecular dynamics for free energy calculations

(2008) Volodymyr Babin et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations

(2008) Jerry B. Abrams et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Advillin Folding Takes Place on a Hypersurface of Small Dimensionality

(2008) Stefano Piana et al.   PHYSICAL REVIEW LETTERS

Dynamical Spatial Warping: A Novel Method for the Conformational Sampling of Biophysical Structure

(2008) Peter Minary et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING