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Theoretical and Computational Chemistry

Working Paper

Validation of AMBER/GAFF for Relative Free Energy Calculations

Lin Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.

Version 1 posted 04 February 2019

1,790

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2

Citations

Theoretical and Computational Chemistry

Working Paper

Molecular Gas Phase Conformational Ensembles

Susanta Das, Kenneth M. Merz, Jr.

Version 3 posted 29 November 2023

465

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Theoretical and Computational Chemistry

Working Paper

Partial to Total Generation of 3D Transition Metal Complexes

Hongni Jin, Kenneth M. Merz

Version 2 posted 31 May 2024

165

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Theoretical and Computational Chemistry

Working Paper

QM/MM Simulations on NVIDIA and AMD GPUs

Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz, Jr

Version 1 posted 30 November 2022

461

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Theoretical and Computational Chemistry

Working Paper

Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization

Alejandro Blanco-Gonzalez, William Betancourt, Ryan Snyder, Shi Zhang, Timothy J. Giese, Andreas W. Goetz, Kenneth M. Merz, Jr., Darrin M. York, Hasan Metin Aktulga, Madushanka Manathunga

Version 1 posted 11 September 2024

196

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Theoretical and Computational Chemistry

Working Paper

Random Forest Refinement of Pairwise Potentials for Protein-ligand Decoy Detection

Jun Pei, Zheng Zheng, Hyunji Kim, Lin Song, Sarah Walworth, Margaux Merz, Kenneth M. Merz Jr.

Version 1 posted 30 April 2019

549

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Theoretical and Computational Chemistry

Working Paper

JAX-ReaxFF: A Gradient Based Framework for Extremely Fast Optimization of Reactive Force Fields

Mehmet Cagri Kaymak, Ali Rahnamoun, Kurt A. O'Hearn, Adri C. T. van Duin, Kenneth M. Merz Jr., Hasan Metin Aktulga

Version 2 posted 03 January 2022

2,434

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Random Forest Refinement of the KECSA2 Knowledge-based Scoring Function for Protein Decoy Detection

Jun Pei, Zheng Zheng, Kenneth M. Merz Jr.

Version 1 posted 22 October 2018

487

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Theoretical and Computational Chemistry

Working Paper

A Polarizable Cationic Dummy Metal Ion Model

Ali Rahnamoun, Kurt A. O'Hearn, Mehmet Cagri Kaymak, Zhen Li, Kenneth M. Merz, Jr., Hasan Metin Aktulga

Version 1 posted 24 January 2022

310

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Theoretical and Computational Chemistry

Working Paper

AutoGraph: Autonomous Graph Based Clustering of Small-Molecule Conformations

Kiyoto Tanemura, Susanta Das, Kenneth M. Merz Jr.

Version 1 posted 29 December 2020

538

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14 results in Kenneth M. Merz in Authors: Kenneth M. Merz

Validation of AMBER/GAFF for Relative Free Energy Calculations

Molecular Gas Phase Conformational Ensembles

Partial to Total Generation of 3D Transition Metal Complexes

QM/MM Simulations on NVIDIA and AMD GPUs

Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization

Random Forest Refinement of Pairwise Potentials for Protein-ligand Decoy Detection

JAX-ReaxFF: A Gradient Based Framework for Extremely Fast Optimization of Reactive Force Fields

Random Forest Refinement of the KECSA2 Knowledge-based Scoring Function for Protein Decoy Detection

A Polarizable Cationic Dummy Metal Ion Model

AutoGraph: Autonomous Graph Based Clustering of Small-Molecule Conformations

14 results in Authors: Kenneth M. Merz