Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator

Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

(2016) Brian K. Radak et al.   JOURNAL OF CHEMICAL PHYSICS

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model

(2015) Yunjie Chen et al.   Journal of Chemical Theory and Computation

Self-guided Langevin dynamics via generalized Langevin equation

(2015) Xiongwu Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal

(2014) Yunjie Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules

(2014) Jeffrey Comer et al.   Journal of Chemical Theory and Computation

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

(2014) Jeffrey Comer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer

(2012) Wei Jiang et al.   Journal of Chemical Theory and Computation

w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations

(2012) Mehrnoosh Arrar et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Toward canonical ensemble distribution from self-guided Langevin dynamics simulation

(2011) Xiongwu Wu et al.   JOURNAL OF CHEMICAL PHYSICS

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

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

(2011) J. P. Nilmeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeting biomolecular flexibility with metadynamics

(2010) Vanessa Leone et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach

(2010) K. Minoukadeh et al.   Journal of Chemical Theory and Computation

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

(2010) Wei Jiang et al.   Journal of Chemical Theory and Computation

Replica exchange with nonequilibrium switches

(2009) A. J. Ballard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Backbone Relaxation Coupled to the Ionization of Internal Groups in Proteins: A Self-Guided Langevin Dynamics Study

(2008) Ana Damjanović et al.   BIOPHYSICAL JOURNAL

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

(2008) Mikolai Fajer et al.   Journal of Chemical Theory and Computation