Hamiltonian replica exchange in GROMACS: a flexible implementation

Computer Folding of RNA Tetraloops? Are We There Yet?

(2013) Petra Kührová et al.   Journal of Chemical Theory and Computation

Folding helical proteins in explicit solvent using dihedral-biased tempering

(2012) C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Replica-exchange method in van der Waals radius space: Overcoming steric restrictions for biomolecules

(2010) Satoru G. Itoh et al.   JOURNAL OF CHEMICAL PHYSICS

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

(2010) Michael S. Lee et al.   Journal of Chemical Theory and Computation

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

(2010) Pavel Banáš 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

On easy implementation of a variant of the replica exchange with solute tempering in GROMACS

(2010) Tsuyoshi Terakawa et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Folding of a Small RNA Hairpin Based on Simulation with Replica Exchange Molecular Dynamics

(2010) Guanghong Zuo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H+Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme

(2010) Vojtěch Mlýnský et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

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

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Reordering Hydrogen Bonds Using Hamiltonian Replica Exchange Enhances Sampling of Conformational Changes in Biomolecular Systems

(2009) Jocelyne Vreede et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations

(2008) Chao Xu et al.   Journal of Chemical Theory and Computation

How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach

(2008) Hugh Nymeyer   Journal of Chemical Theory and Computation

Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange

(2008) Martin Zacharias   Journal of Chemical Theory and Computation

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

(2008) Mikolai Fajer et al.   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

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

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin

(2007) Angel E. Garcia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY