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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.

438

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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.

443

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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.

704

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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

1,553

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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

2,027

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1

Citations

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

300

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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

459

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1

Citations

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.

1,700

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2

Citations

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.

516

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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

228

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11 results in Kenneth M. Merz Jr. in Authors: Kenneth M. Merz Jr.

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

AutoGraph: Autonomous Graph Based Clustering of Small-Molecule Conformations

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

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

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

QM/MM Simulations on NVIDIA and AMD GPUs

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

Validation of AMBER/GAFF for Relative Free Energy Calculations

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

A Polarizable Cationic Dummy Metal Ion Model

11 results in Authors: Kenneth M. Merz Jr.