Hamiltonian based resonance-free approach for enabling very large time steps in multiple time-scale molecular dynamics

Molecular Dynamics with Very Large Time Steps for the Calculation of Solvation Free Energies

(2020) Charlles R. A. Abreu et al.   Journal of Chemical Theory and Computation

Refinement of thermostated molecular dynamics using backward error analysis

(2019) Ana J. Silveira et al.   JOURNAL OF CHEMICAL PHYSICS

A Unified Efficient Thermostat Schemefor the Canonical Ensemblewith Holonomic or Isokinetic Constraints via Molecular Dynamics

(2019) Zhijun Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems

(2018) Josh Fass et al.   Entropy

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

(2018) Pei-Yang Chen 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

Stationary state distribution and efficiency analysis of the Langevin equation via real or virtual dynamics

(2017) Dezhang Li et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular dynamics with rigid bodies: Alternative formulation and assessment of its limitations when employed to simulate liquid water

(2017) Ana J. Silveira et al.   JOURNAL OF CHEMICAL PHYSICS

The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations

(2017) Tanfeng Zhao et al.   Journal of Chemical Theory and Computation

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method

(2016) Adrien Lesage et al.   JOURNAL OF PHYSICAL CHEMISTRY B

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

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

Free Energy Reconstruction from Metadynamics or Adiabatic Free Energy Dynamics Simulations

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

How Accurately Do Current Force Fields Predict Experimental Peptide Conformations? An Adiabatic Free Energy Dynamics Study

(2014) Alexandar T. Tzanov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Erratum: “Heating and flooding: A unified approach for rapid generation of free energy surfaces” [J. Chem. Phys. 137, 024102 (2012)]

(2013) Ming Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Robust and efficient configurational molecular sampling via Langevin dynamics

(2013) Benedict Leimkuhler et al.   JOURNAL OF CHEMICAL PHYSICS

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

(2013) Joseph E. Basconi 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

Using Nonequilibrium Fluctuation Theorems to Understand and Correct Errors in Equilibrium and Nonequilibrium Simulations of Discrete Langevin Dynamics

(2013) David A. Sivak et al.   Physical Review X

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

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

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

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

Equipartition and the Calculation of Temperature in Biomolecular Simulations

(2010) Michael P. Eastwood et al.   Journal of Chemical Theory and Computation

Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls

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

Discretization errors in molecular dynamics simulations with deterministic and stochastic thermostats

(2010) Ruslan L. Davidchack   JOURNAL OF COMPUTATIONAL PHYSICS

Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides — The Alanine Dipeptide Case Study

(2010) Jiří Vymětal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Gentle Stochastic Thermostat for Molecular Dynamics

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

On the generalized equipartition theorem in molecular dynamics ensembles and the microcanonical thermodynamics of small systems

(2008) Mark J. Uline 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