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Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

Journal of chemical theory and computation, 2015-04, Vol.11 (4), p.1864-1874

2015

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Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

Biophysical journal, 2015-03, Vol.108 (5), p.1153-1164

2015

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An overview of the Amber biomolecular simulation package

Wiley interdisciplinary reviews. Computational molecular science, 2013-03, Vol.3 (2), p.198-210

2013

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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

Journal of chemical information and modeling, 2018-10, Vol.58 (10), p.2043-2050

2018

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Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

Journal of chemical theory and computation, 2014-07, Vol.10 (7), p.2677-2689

2014

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CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

Proceedings of the National Academy of Sciences - PNAS, 2017-07, Vol.114 (28), p.7260-7265

2017

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mRNA codon optimization with quantum computers

PloS one, 2021-10, Vol.16 (10), p.e0259101-e0259101

2021

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LIPID11: A Modular Framework for Lipid Simulations Using Amber

The journal of physical chemistry. B, 2012-09, Vol.116 (36), p.11124-11136

2012

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Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

Journal of computational chemistry, 2016-08, Vol.37 (21), p.2029-2037

2016

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GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Soft matter, 2012-01, Vol.8 (37), p.9617-9627

2012

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implementation of a fast and accurate QM/MM potential method in Amber

Journal of computational chemistry, 2008-05, Vol.29 (7), p.1019-1031

2008

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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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RNA folding using quantum computers

PLoS computational biology, 2022-04, Vol.18 (4), p.e1010032-e1010032

2022

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Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

Journal of chemical theory and computation, 2013-09, Vol.9 (9), p.4131-4139

2013

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Mechanism of 150-cavity formation in influenza neuraminidase

Nature communications, 2011-07, Vol.2 (1), p.388-388, Article 388

2011

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Lipid21: Complex Lipid Membrane Simulations with AMBER

Journal of chemical theory and computation, 2022-03, Vol.18 (3), p.1726-1736

2022

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Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations

ACS central science, 2016-10, Vol.2 (10), p.756-763

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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Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2007-07, Vol.111 (26), p.5655-5664

2007

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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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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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Complement Factor H and Simian Virus 40 bind the GM1 ganglioside in distinct conformations

Glycobiology (Oxford), 2016-05, Vol.26 (5), p.532-539

2016

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

Journal of chemical theory and computation, 2012-05, Vol.8 (5), p.1542-1555

2012

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Paramfit: Automated optimization of force field parameters for molecular dynamics simulations

Journal of computational chemistry, 2015-01, Vol.36 (2), p.79-87

2015

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Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations

Biochimica et biophysica acta, 2016-09, Vol.1857 (9), p.1594-1606

2016

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Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

An overview of the Amber biomolecular simulation package

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

mRNA codon optimization with quantum computers

LIPID11: A Modular Framework for Lipid Simulations Using Amber

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

implementation of a fast and accurate QM/MM potential method in Amber

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

RNA folding using quantum computers

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

Mechanism of 150-cavity formation in influenza neuraminidase

Lipid21: Complex Lipid Membrane Simulations with AMBER

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations

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

Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package

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

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

Complement Factor H and Simian Virus 40 bind the GM1 ganglioside in distinct conformations

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

Paramfit: Automated optimization of force field parameters for molecular dynamics simulations

Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations

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