| The Amber biomolecular simulation programs | journal | January 2005 | 
    | CHARMM: The biomolecular simulation program | journal | July 2009 | 
    | Large-scale, long-term nonadiabatic electron molecular dynamics for describing material properties and phenomena in extreme environments | journal | September 2010 | 
    | Viscoplasticity using peridynamics | journal | January 2009 | 
    | Adaptive machine learning framework to accelerate ab initio molecular dynamics | journal | December 2014 | 
    | Fast Parallel Algorithms for Short-Range Molecular Dynamics | journal | March 1995 | 
    | Software components for parallel multiscale simulation: an example with LAMMPS | journal | December 2009 | 
    | Particle shape effects in discrete element modelling of cohesive angular particles | journal | October 2010 | 
    | The potential of atomistic simulations and the knowledgebase of interatomic models | journal | July 2011 | 
    | A Computational Algorithm to Produce Virtual X-ray and Electron Diffraction Patterns from Atomistic Simulations | journal | January 2014 | 
    | Particle dynamics modeling methods for colloid suspensions | journal | May 2014 | 
    | SEM++: A particle model of cellular growth, signaling and migration | journal | May 2014 | 
    | DEM simulations of polydisperse media: efficient contact detection applied to investigate the quasi-static limit | journal | September 2020 | 
    | Vectorized link cell Fortran code for molecular dynamics simulations for a large number of particles | journal | October 1989 | 
    | Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems | journal | June 1996 | 
    | Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations | journal | October 1983 | 
    | VMD: Visual molecular dynamics | journal | February 1996 | 
    | Systematic analysis of local atomic structure combined with 3D computer graphics | journal | March 1994 | 
    | A Gay–Berne potential for dissimilar biaxial particles | journal | November 1998 | 
    | Replica-exchange molecular dynamics method for protein folding | journal | November 1999 | 
    | Simulation of low index rutile surfaces with a transferable variable-charge Ti–O interatomic potential and comparison with ab initio results | journal | April 2002 | 
    | Automated scientific software scripting with SWIG | journal | July 2003 | 
    | Accelerated Molecular Dynamics Methods: Introduction and Recent Developments | book | January 2009 | 
    | A Method for Molecular Dynamics on Curved Surfaces | journal | March 2016 | 
    | A multiscale coarse-grained model of the SARS-CoV-2 virion | journal | March 2021 | 
    | LAMMPS implementation of rapid artificial neural network derived interatomic potentials | journal | August 2021 | 
    | Developing community codes for materials modeling | journal | December 2013 | 
    | Structural characterization of deformed crystals by analysis of common atomic neighborhood | journal | September 2007 | 
    | Accurate and efficient methods for modeling colloidal mixtures in an explicit solvent using molecular dynamics | journal | September 2008 | 
    | Implementing peridynamics within a molecular dynamics code | journal | December 2008 | 
    | Implementing molecular dynamics on hybrid high performance computers – short range forces | journal | April 2011 | 
    | Phonon dispersion measured directly from molecular dynamics simulations | journal | October 2011 | 
    | Implementing molecular dynamics on hybrid high performance computers – Particle–particle particle-mesh | journal | March 2012 | 
    | Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions | journal | December 2012 | 
    | Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid | journal | August 2013 | 
    | Implementing molecular dynamics on hybrid high performance computers—Three-body potentials | journal | December 2013 | 
    | PLUMED 2: New feathers for an old bird | journal | February 2014 | 
    | Adaptive dynamic load-balancing with irregular domain decomposition for particle simulations | journal | May 2015 | 
    | Optimizing legacy molecular dynamics software with directive-based offload | journal | October 2015 | 
    | Method for finding mechanism and activation energy of magnetic transitions, applied to skyrmion and antivortex annihilation | journal | November 2015 | 
    | DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics | journal | July 2018 | 
    | Incorporating surface polarization effects into large-scale coarse-grained Molecular Dynamics simulation | journal | August 2019 | 
    | Aspherical particle models for molecular dynamics simulation | journal | October 2019 | 
    | PANNA: Properties from Artificial Neural Network Architectures | journal | November 2020 | 
    | The MolSSI Driver Interface Project: A framework for standardized, on-the-fly interoperability between computational molecular sciences codes | journal | April 2021 | 
    | Fast and robust algorithm for energy minimization of spin systems applied in an analysis of high temperature spin configurations in terms of skyrmion density | journal | March 2021 | 
    | Characteristics of dynamic brittle fracture captured with peridynamics | journal | April 2011 | 
    | Modeling shockwaves and impact phenomena with Eulerian peridynamics | journal | September 2017 | 
    | Smooth particle hydrodynamics simulation of damage induced by a spherical indenter scratching a viscoplastic material | journal | March 2016 | 
    | Energy-conserving dissipative particle dynamics with temperature-dependent properties | journal | May 2014 | 
    | Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials | journal | March 2015 | 
    | Massively parallel symplectic algorithm for coupled magnetic spin dynamics and molecular dynamics | journal | November 2018 | 
    | Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics | journal | May 2021 | 
    | Energy surface and lifetime of magnetic skyrmions | journal | August 2018 | 
    | Rendezvous algorithms for large-scale modeling and simulation | journal | January 2021 | 
    | Classical atomistic simulations of surfaces and heterogeneous interfaces with the charge-optimized many body (COMB) potentials | journal | September 2013 | 
    | Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques | journal | April 2012 | 
    | Vibration induced flow in hoppers: DEM 2D polygon model | journal | December 2008 | 
    | Modeling chemical reactions in classical molecular dynamics simulations | journal | October 2017 | 
    | On the nature of the magnetocaloric effect of the first-order magnetostructural transition | journal | September 2012 | 
    | GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers | journal | September 2015 | 
    | Peridynamic model for microballistic perforation of multilayer graphene | journal | June 2021 | 
    | Long-Time Dynamics through Parallel Trajectory Splicing | journal | December 2015 | 
    | Parallel Multistream Training of High-Dimensional Neural Network Potentials | journal | April 2019 | 
    | Explicit Multielement Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems | journal | May 2020 | 
    | Performance and Cost Assessment of Machine Learning Interatomic Potentials | journal | October 2019 | 
    | REACTER: A Heuristic Method for Reactive Molecular Dynamics | journal | November 2020 | 
    | Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins | journal | August 2013 | 
    | Versatile Object-Oriented Toolkit for Coarse-Graining Applications | journal | November 2009 | 
    | Charge equilibration for molecular dynamics simulations | journal | April 1991 | 
    | Electronegativity-equalization method for the calculation of atomic charges in molecules | journal | July 1986 | 
    | Electronegativity equalization: application and parametrization | journal | February 1985 | 
    | Electronegativity and bond energy | journal | April 1983 | 
    | Markov State Models: From an Art to a Science | journal | February 2018 | 
    | ReaxFF:  A Reactive Force Field for Hydrocarbons | journal | October 2001 | 
    | ReaxFF SiO Reactive Force Field for Silicon and Silicon Oxide Systems | journal | May 2003 | 
    | Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation | journal | May 2003 | 
    | Mapping Atomistic Simulations to Mesoscopic Models:  A Systematic Coarse-Graining Procedure for Vinyl Polymer Chains | journal | October 2005 | 
    | Prebiotic Chemistry within a Simple Impacting Icy Mixture | journal | May 2013 | 
    | ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation | journal | February 2008 | 
    | Temperature-Dependent Elasticity of a Semicrystalline Interphase Composed of Freely Rotating Chains | journal | September 2003 | 
    | Probing the limits of metal plasticity with molecular dynamics simulations | journal | September 2017 | 
    | Piezomagnetism and magnetoelastic memory in uranium dioxide | journal | July 2017 | 
    | Evidence for percolation diffusion of cations and reordering in disordered pyrochlore from accelerated molecular dynamics | journal | September 2017 | 
    | Physically informed artificial neural networks for atomistic modeling of materials | journal | May 2019 | 
    | Anomalous collapses of Nares Strait ice arches leads to enhanced export of Arctic sea ice | journal | January 2021 | 
    | Uncertainty quantification in molecular simulations with dropout neural network potentials | journal | August 2020 | 
    | Performant implementation of the atomic cluster expansion (PACE) and application to copper and silicon | journal | June 2021 | 
    | Electric and antiferromagnetic chiral textures at multiferroic domain walls | journal | November 2019 | 
    | Using metadynamics to explore complex free-energy landscapes | journal | March 2020 | 
    | Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations | journal | January 2014 | 
    | Catastrophic depolymerization of microtubules driven by subunit shape change | journal | January 2018 | 
    | DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism | journal | January 2006 | 
    | A climbing image nudged elastic band method for finding saddle points and minimum energy paths | journal | December 2000 | 
    | Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm | journal | August 2003 | 
    | Equilibration of long chain polymer melts in computer simulations | journal | December 2003 | 
    | Coarse-grained simulations of lipid bilayers | journal | December 2004 | 
    | Efficient particle labeling in atomistic simulations | journal | March 2007 | 
    | P3M algorithm for dipolar interactions | journal | December 2008 | 
    | VORO++ : A three-dimensional Voronoi cell library in C++ | journal | December 2009 | 
    | General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions | journal | October 2009 | 
    | A two-temperature model of radiation damage in α-quartz | journal | October 2010 | 
    | Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model | journal | February 2011 | 
    | Electronegativity: The density functional viewpoint | journal | April 1978 | 
    | Molecular dynamics of polymeric systems | journal | February 1979 | 
    | Dynamics of entangled linear polymer melts:  A molecular‐dynamics simulation | journal | April 1990 | 
    | Reversible multiple time scale molecular dynamics | journal | August 1992 | 
    | Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems | journal | June 1993 | 
    | Diffusion in Lennard‐Jones fluids using dual control volume grand canonical molecular dynamics simulation (DCV‐GCMD) | journal | May 1994 | 
    | Dynamical fluctuating charge force fields: Application to liquid water | journal | October 1994 | 
    | A smooth particle mesh Ewald method | journal | November 1995 | 
    | A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity | journal | April 1997 | 
    | A method for accelerating the molecular dynamics simulation of infrequent events | journal | March 1997 | 
    | Sequence-dependent thermodynamics of a coarse-grained DNA model | journal | October 2012 | 
    | Computer simulations of bilayer membranes: Self-assembly and interfacial tension | journal | May 1998 | 
    | Development and application of a particle-particle particle-mesh Ewald method for dispersion interactions | journal | November 2012 | 
    | How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines | journal | November 1998 | 
    | Mesoscopic model for solvent dynamics | journal | May 1999 | 
    | A reactive potential for hydrocarbons with intermolecular interactions | journal | April 2000 | 
    | Temperature-accelerated dynamics for simulation of infrequent events | journal | June 2000 | 
    | Perspective: Coarse-grained models for biomolecular systems | journal | September 2013 | 
    | Periodic boundary conditions for long-time nonequilibrium molecular dynamics simulations of incompressible flows | journal | November 2014 | 
    | Direct simulation Monte Carlo investigation of the Richtmyer-Meshkov instability | journal | August 2015 | 
    | Molecular simulation of flow-enhanced nucleation in n -eicosane melts under steady shear and uniaxial extension | journal | December 2016 | 
    | Extending the accuracy of the SNAP interatomic potential form | journal | June 2018 | 
    | Importance of corners in fracture of highly crosslinked polymeric adhesives | journal | November 2018 | 
    | Classical Pauli repulsion: An anisotropic, atomic multipole model | journal | February 2019 | 
    | Direct simulation Monte Carlo on petaflop supercomputers and beyond | journal | August 2019 | 
    | DFTB+, a software package for efficient approximate density functional theory based atomistic simulations | journal | March 2020 | 
    | Scalable molecular dynamics on CPU and GPU architectures with NAMD | journal | July 2020 | 
    | Neural network potential from bispectrum components: A case study on crystalline silicon | journal | August 2020 | 
    | Using collective variables to drive molecular dynamics simulations | journal | December 2013 | 
    | Highly scalable discrete-particle simulations with novel coarse-graining: accessing the microscale | journal | May 2018 | 
    | Comparison of modern Langevin integrators for simulations of coarse-grained polymer melts | journal | August 2019 | 
    | Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble | journal | July 1987 | 
    | Monte Carlo simulation of multicomponent equilibria in a semigrand canonical ensemble | journal | August 1988 | 
    | Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants | journal | January 2007 | 
    | A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons | journal | January 2002 | 
    | Including the effects of electronic stopping and electron–ion interactions in radiation damage simulations | journal | December 2006 | 
    | The effect of electron–ion interactions on radiation damage simulations | journal | November 2007 | 
    | Shell model simulations by adiabatic dynamics | journal | February 1993 | 
    | Robust structural identification via polyhedral template matching | journal | May 2016 | 
    | Efficient optimization method for finding minimum energy paths of magnetic transitions | journal | May 2020 | 
    | Beryllium-driven structural evolution at the divertor surface | journal | March 2021 | 
    | Dynamics of Radiation Damage | journal | November 1960 | 
    | Correlations in the Motion of Atoms in Liquid Argon | journal | October 1964 | 
    | Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules | journal | July 1967 | 
    | Nonlinear-response theory for steady planar Couette flow | journal | September 1984 | 
    | Atomic cluster expansion of scalar, vectorial, and tensorial properties including magnetism and charge transfer | journal | July 2020 | 
    | Size- and temperature-dependent magnetization of iron nanoclusters | journal | November 2020 | 
    | Spin-lattice model for cubic crystals | journal | March 2021 | 
    | Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals | journal | June 1984 | 
    | New empirical approach for the structure and energy of covalent systems | journal | April 1988 | 
    | Semiempirical modified embedded-atom potentials for silicon and germanium | journal | September 1989 | 
    | Modified embedded-atom potentials for cubic materials and impurities | journal | August 1992 | 
    | Molecular-dynamics simulations of void collapse in shocked model-molecular solids | journal | June 1994 | 
    | Electrostatic potentials for metal-oxide surfaces and interfaces | journal | October 1994 | 
    | Spin dynamics in magnets: Equation of motion and finite temperature effects | journal | July 1996 | 
    | Dislocation nucleation and defect structure during surface indentation | journal | November 1998 | 
    | Analytic bond-order potentials beyond Tersoff-Brenner. I. Theory | journal | April 1999 | 
    | Modified charge transfer–embedded atom method potential for metal/metal oxide systems | journal | January 2004 | 
    | Empirical variable-charge models for titanium oxides: A study in transferability | journal | April 2004 | 
    | Constant-stress Hugoniostat method for following the dynamical evolution of shocked matter | journal | July 2004 | 
    | Analytic bond-order potential for the gallium arsenide system | journal | January 2006 | 
    | Use of a variable-charge interatomic potential for atomistic simulations of bulk, oxygen vacancies, and surfaces of rutile TiO 2 | journal | April 2006 | 
    | Charge optimized many-body potential for the Si ∕ SiO 2 system | journal | February 2007 | 
    | Large-scale simulation of the spin-lattice dynamics in ferromagnetic iron | journal | July 2008 | 
    | Charge-optimized many-body potential for the hafnium/hafnium oxide system | journal | March 2010 | 
    | Analytical bond-order potential for the cadmium telluride binary system | journal | March 2012 | 
    | Dynamic magnetocaloric effect in bcc iron and hcp gadolinium | journal | July 2014 | 
    | Multiscale modeling of shock wave localization in porous energetic material | journal | January 2018 | 
    | Group-theoretical high-order rotational invariants for structural representations: Application to linearized machine learning interatomic potential | journal | June 2019 | 
    | Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids | journal | May 1999 | 
    | Smoothed dissipative particle dynamics | journal | February 2003 | 
    | Interaction potentials for soft and hard ellipsoids | journal | April 2003 | 
    | Hydrodynamic interactions and Brownian forces in colloidal suspensions: Coarse-graining over time and length scales | journal | September 2006 | 
    | Application of atomic stress to compute heat flux via molecular dynamics for systems with many-body interactions | journal | May 2019 | 
    | Gaussian Approximation Potentials: The Accuracy of Quantum Mechanics, without the Electrons | journal | April 2010 | 
    | Magnetostructural Transition Kinetics in Shocked Iron | journal | August 2016 | 
    | Charge Regulation Effects in Nanoparticle Self-Assembly | journal | March 2021 | 
    | Unified Approach for Molecular Dynamics and Density-Functional Theory | journal | November 1985 | 
    | Algorithm for Molecular Dynamics Simulations of Spin Liquids | journal | January 2001 | 
    | Structural Relaxation Made Simple | journal | October 2006 | 
    | Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces | journal | April 2007 | 
    | The Design and Implementation of FFTW3 | journal | February 2005 | 
    | The Kokkos EcoSystem: Comprehensive Performance Portability For High Performance Computing | journal | January 2021 | 
    | A Partitioning Strategy for Nonuniform Problems on Multiprocessors | journal | May 1987 | 
    | Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems | journal | August 2008 | 
    | Moment Tensor Potentials: A Class of Systematically Improvable Interatomic Potentials | journal | January 2016 | 
    | Coarse-grained simulation of DNA using LAMMPS: An implementation of the oxDNA model and its applications | journal | May 2018 | 
    | Large-Scale Molecular-Dynamics Simulation of 19 Billion Particles | journal | January 2004 | 
    | Smoothed Particle Hydrodynamics and Its Diverse Applications | journal | January 2012 | 
    | Simulating Microscopic Hydrodynamic Phenomena with Dissipative Particle Dynamics | journal | June 1992 | 
    | Probing eukaryotic cell mechanics via mesoscopic simulations | journal | September 2017 | 
    | Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA | journal | July 2015 | 
    | Models, algorithms and validation for opensource DEM and CFD-DEM | journal | January 2012 | 
    | Computational aspects of many-body potentials | journal | May 2012 |