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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

536

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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

2,310

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1

Citations

Theoretical and Computational Chemistry

Working Paper

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

Madushanka Manathunga, Yipu Miao, Dawei Mu, Andreas Goetz, Kenneth M. Merz Jr.

Version 1 posted 24 March 2020

729

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Theoretical and Computational Chemistry

Working Paper

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

Madushanka Manathunga, Chi Jin, Vinicius Cruzeiro, Yipu Miao, Dawei Mu, Kamesh Arumugam, Kristopher Keipert, Hasan Metin Aktulga, Kenneth M. Merz, Jr., Andreas Goetz

Version 1 posted 10 February 2021

530

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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

463

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Theoretical and Computational Chemistry

Working Paper

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

Vinicius Cruzeiro, Madushanka Manathunga, Kenneth M. Merz, Jr., Andreas Goetz

Version 1 posted 16 February 2021

1,876

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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

1,760

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2

Citations

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

513

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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

425

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Organometallic Chemistry

Working Paper

LigandDiff: 3D Transition Metal Complex Generation with Diffusion Models

Hongni Jin, Kenneth M. Merz, Jr

Version 1 posted 13 February 2024

370

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12 results in Kenneth M. Merz, Jr. in Authors: Kenneth M. Merz, Jr.

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

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

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

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

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

Validation of AMBER/GAFF for Relative Free Energy Calculations

AutoGraph: Autonomous Graph Based Clustering of Small-Molecule Conformations

QM/MM Simulations on NVIDIA and AMD GPUs

LigandDiff: 3D Transition Metal Complex Generation with Diffusion Models

12 results in Authors: Kenneth M. Merz, Jr.