Spectral gap optimization of order parameters for sampling complex molecular systems

Metainference: A Bayesian inference method for heterogeneous systems

(2016) M. Bonomi et al.   Science Advances

Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes

(2015) Purushottam D. Dixit 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

Role of water and steric constraints in the kinetics of cavity–ligand unbinding

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

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

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

(2014) Matteo Salvalaglio et al.   Journal of Chemical Theory and Computation

Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model

(2014) Edina Rosta et al.   Journal of Chemical Theory and Computation

A Time-Independent Free Energy Estimator for Metadynamics

(2014) Pratyush Tiwary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

PLUMED 2: New feathers for an old bird

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

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Accelerated molecular dynamics through stochastic iterations and collective variable based basin identification

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW B

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

(2013) D. Granata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles of maximum entropy and maximum caliber in statistical physics

(2013) Steve Pressé et al.   REVIEWS OF MODERN PHYSICS

Parameter Space Compression Underlies Emergent Theories and Predictive Models

(2013) B. B. Machta et al.   SCIENCE

Metadynamics with Adaptive Gaussians

(2012) Davide Branduardi et al.   Journal of Chemical Theory and Computation

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Time scale separation leads to position-dependent diffusion along a slow coordinate

(2011) Alexander Berezhkovskii et al.   JOURNAL OF CHEMICAL PHYSICS

Interplay between Hydrodynamics and the Free Energy Surface in the Assembly of Nanoscale Hydrophobes

(2011) Joseph A. Morrone et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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 Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

(2009) Fabrizio Marinelli et al.   PLoS Computational Biology

Dewetting and Hydrophobic Interaction in Physical and Biological Systems

(2008) Bruce J. Berne et al.   Annual Review of Physical Chemistry

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve 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

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems

(2008) R. R. Coifman et al.   MULTISCALE MODELING & SIMULATION

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

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

(2008) L. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA