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Toward Chemical Accuracy in the Description of Ion–Water Interactions through Many-Body Representations. I. Halide–Water Dimer Potential Energy Surfaces

Journal of chemical theory and computation, 2016-06, Vol.12 (6), p.2698-2705

2016

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Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

Journal of chemical theory and computation, 2013-09, Vol.9 (9), p.3878-3888

2013

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Solvation Free Energies and Adsorption Energies at the Metal/Water Interface from Hybrid Quantum-Mechanical/Molecular Mechanics Simulations

Journal of chemical theory and computation, 2020-10, Vol.16 (10), p.6539-6549

2020

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On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

The Journal of chemical physics, 2016-11, Vol.145 (19), p.194504-194504

2016

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Monitoring Water Clusters “Melt” Through Vibrational Spectroscopy

Journal of the American Chemical Society, 2017-05, Vol.139 (20), p.7082-7088

2017

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Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions

The Journal of chemical physics, 2018-06, Vol.148 (24), p.241725-241725

2018

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Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units

Journal of chemical information and modeling, 2023-02, Vol.63 (3), p.711-717

2023

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Geometry Optimization: A Comparison of Different Open-Source Geometry Optimizers

Journal of chemical theory and computation, 2023-11, Vol.19 (21), p.7533-7541

2023

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Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

Journal of chemical information and modeling, 2021-05, Vol.61 (5), p.2109-2115

2021

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Force Field for Water over Pt(111): Development, Assessment, and Comparison

Journal of chemical theory and computation, 2018-06, Vol.14 (6), p.3238-3251

2018

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Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein

Journal of chemical theory and computation, 2012-12, Vol.8 (12), p.5092-5106

2012

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The Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies

Journal of the American Chemical Society, 2014-01, Vol.136 (1), p.321-329

2014

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Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program

Journal of chemical theory and computation, 2020-07, Vol.16 (7), p.4315-4326

2020

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AmberTools

Journal of chemical information and modeling, 2023-10, Vol.63 (20), p.6183-6191

2023

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ReaxFF/AMBERA Framework for Hybrid Reactive/Nonreactive Force Field Molecular Dynamics Simulations

Journal of chemical theory and computation, 2020-12, Vol.16 (12), p.7645-7654

2020

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DFT Fea3–O/O–O Vibrational Frequency Calculations over Catalytic Reaction Cycle States in the Dinuclear Center of Cytochrome c Oxidase

Inorganic chemistry, 2019-10, Vol.58 (20), p.13933-13944

2019

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Harnessing the Power of Multi-GPU Acceleration into the Quantum Interaction Computational Kernel Program

Journal of chemical theory and computation, 2021-07, Vol.17 (7), p.3955-3966

2021

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Performance of Kinetic Energy Functionals for Interaction Energies in a Subsystem Formulation of Density Functional Theory

Journal of chemical theory and computation, 2009-12, Vol.5 (12), p.3161-3174

2009

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Highly Accurate Many-Body Potentials for Simulations of N2O5 in Water: Benchmarks, Development, and Validation

Journal of chemical theory and computation, 2021-07, Vol.17 (7), p.3931-3945

2021

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Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials

The Journal of chemical physics, 2024-06, Vol.160 (22)

2024

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Linking Chemical Electron–Proton Transfer to Proton Pumping in Cytochrome c Oxidase: Broken-Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron–Copper Dinuclear Complex

Inorganic chemistry, 2014-07, Vol.53 (13), p.6458-6472

2014

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The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

Journal of computational chemistry, 2015-04, Vol.36 (9), p.633-648

2015

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Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems

Journal of chemical theory and computation, 2012-08, Vol.8 (8), p.2868-2877

2012

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A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus

Physical chemistry chemical physics : PCCP, 2016-08, Vol.18 (31), p.21162-21171

2016

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

Computer physics communications, 2013-02, Vol.184 (2), p.374-380

2013

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Toward Chemical Accuracy in the Description of Ion–Water Interactions through Many-Body Representations. I. Halide–Water Dimer Potential Energy Surfaces

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

Solvation Free Energies and Adsorption Energies at the Metal/Water Interface from Hybrid Quantum-Mechanical/Molecular Mechanics Simulations

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

Monitoring Water Clusters “Melt” Through Vibrational Spectroscopy

Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions

Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units

Geometry Optimization: A Comparison of Different Open-Source Geometry Optimizers

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

Force Field for Water over Pt(111): Development, Assessment, and Comparison

Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein

The Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies

Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program

AmberTools

ReaxFF/AMBERA Framework for Hybrid Reactive/Nonreactive Force Field Molecular Dynamics Simulations

DFT Fea3–O/O–O Vibrational Frequency Calculations over Catalytic Reaction Cycle States in the Dinuclear Center of Cytochrome c Oxidase

Harnessing the Power of Multi-GPU Acceleration into the Quantum Interaction Computational Kernel Program

Performance of Kinetic Energy Functionals for Interaction Energies in a Subsystem Formulation of Density Functional Theory

Highly Accurate Many-Body Potentials for Simulations of N2O5 in Water: Benchmarks, Development, and Validation

Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials

Linking Chemical Electron–Proton Transfer to Proton Pumping in Cytochrome c Oxidase: Broken-Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron–Copper Dinuclear Complex

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems

A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus

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

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