Calculation of free energy landscapes: A histogram reweighted metadynamics approach

Linking Well-Tempered Metadynamics Simulations with Experiments

(2010) Alessandro Barducci et al.   BIOPHYSICAL JOURNAL

Conformational free energies of methyl-α-L-iduronic and methyl-β-D-glucuronic acids in water

(2010) Volodymyr Babin et al.   JOURNAL OF CHEMICAL PHYSICS

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

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics

(2009) M. Bonomi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Positive Feedback between Transcriptional and Kinase Suppression in Nematodes with Extraordinary Longevity and Stress Resistance

(2009) Çagdaþ Tazearslan et al.   PLoS Genetics

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide

(2008) Birgit Strodel et al.   CHEMICAL PHYSICS LETTERS

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Estimation of microscopic averages from metadynamics

(2008) G. Tiana   EUROPEAN PHYSICAL JOURNAL B

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

Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes

(2008) Vojtěch Spiwok et al.   JOURNAL OF MOLECULAR MODELING

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the potential energy landscape of glass-forming systems: from inherent structures via metabasins to macroscopic transport

(2008) Andreas Heuer   JOURNAL OF PHYSICS-CONDENSED MATTER

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

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS