Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform

Enhanced sampling techniques in molecular dynamics simulations of biological systems

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

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model

(2015) Marie L. Laury et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field

(2014) Jayvee R. Abella et al.   Journal of Chemical Theory and Computation

PLUMED 2: New feathers for an old bird

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

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units

(2013) Steffen Lindert et al.   Journal of Chemical Theory and Computation

Mechanism of AMPPD Chemiluminescence in a Different Voice

(2013) Ling Yue et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations

(2010) C. Mark Maupin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics

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

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

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