Molecular dynamics based enhanced sampling of collective variables with very large time steps

Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

(2017) Shalini Awasthi et al.   JOURNAL OF CHEMICAL PHYSICS

A unified thermostat scheme for efficient configurational sampling for classical/quantum canonical ensembles via molecular dynamics

(2017) Zhijun Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes

(2017) Eliodoro Chiavazzo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Stochastic, Resonance-Free Multiple Time-Step Algorithm for Polarizable Models That Permits Very Large Time Steps

(2016) Daniel T. Margul et al.   Journal of Chemical Theory and Computation

Prediction of Protein–Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations

(2016) Anthony J. Clark et al.   Journal of Chemical Theory and Computation

Advanced Potential Energy Surfaces for Molecular Simulation

(2016) Alex Albaugh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring polymorphism of benzene and naphthalene with free energy based enhanced molecular dynamics

(2016) Elia Schneider et al.   Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials

Report on the sixth blind test of organic crystal structure prediction methods

(2016) Anthony M. Reilly et al.   Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials

Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions

(2014) Tang-Qing Yu et al.   JOURNAL OF CHEMICAL PHYSICS

Free Energy Reconstruction from Metadynamics or Adiabatic Free Energy Dynamics Simulations

(2014) Michel A. Cuendet et al.   Journal of Chemical Theory and Computation

Microscopic mechanisms of equilibrium melting of a solid

(2014) A. Samanta et al.   SCIENCE

Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble

(2013) Omar Valsson et al.   Journal of Chemical Theory and Computation

Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps

(2013) Ben Leimkuhler et al.   MOLECULAR PHYSICS

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

(2012) Ming Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Metadynamics with Adaptive Gaussians

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

Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances

(2011) Joseph A. Morrone et al.   JOURNAL OF CHEMICAL PHYSICS

Temperature-Accelerated Method for Exploring Polymorphism in Molecular Crystals Based on Free Energy

(2011) Tang-Qing Yu et al.   PHYSICAL REVIEW LETTERS

Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls

(2010) Joseph A. Morrone et al.   Journal of Chemical Theory and Computation

Enhanced Sampling in the Well-Tempered Ensemble

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

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

A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1

(2009) Fabio Pietrucci et al.   Journal of Chemical Theory and Computation

A Gentle Stochastic Thermostat for Molecular Dynamics

(2009) Ben Leimkuhler et al.   JOURNAL OF STATISTICAL PHYSICS

Efficient Method for Predicting Crystal Structures at Finite Temperature: Variable Box Shape Simulations

(2009) Laura Filion et al.   PHYSICAL REVIEW LETTERS

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

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

The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin

(2008) Massimiliano Bonomi 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