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

Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics – Monte Carlo Canonical Propagation Algorithm

(2016) Yunjie Chen 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

Efficient molecular dynamics using geodesic integration and solvent–solute splitting

(2016) Benedict Leimkuhler et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Efficient treatment of induced dipoles

(2015) Andrew C. Simmonett et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald

(2014) Andrew C. Simmonett et al.   JOURNAL OF CHEMICAL PHYSICS

Building Force Fields: An Automatic, Systematic, and Reproducible Approach

(2014) Lee-Ping Wang et al.   Journal of Physical Chemistry Letters

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

(2013) Cameron Abrams et al.   Entropy

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes 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

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

(2013) Ben Leimkuhler et al.   MOLECULAR PHYSICS

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz 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

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

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

(2011) John D. Chodera et al.   JOURNAL OF CHEMICAL PHYSICS

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

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

(2009) Peter Eastman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY