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Theoretical and Computational Chemistry

Working Paper

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli

Version 1 posted 23 August 2019

1,857

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5

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Biological and Medicinal Chemistry

Working Paper

A Fast Implementation of the Nudged Elastic Band Method in AMBER

Delaram Ghoreishi, David Cerutti, Zachary Fallon, Carlos Simmerling, Adrian Roitberg

Version 1 posted 18 June 2019

808

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Theoretical and Computational Chemistry

Working Paper

TORO Indexer: A PyTorch-Based Indexing Algorithm for kHz Serial Crystallography

Piero Gasparotto, Luis Barba, Hans-Christian Stadler, Greta Assmann, Henrique Mendonça, Alun Ashton, Markus Janousch, Filip Leonarski, Benjamı́n Béjar

Version 1 posted 06 November 2023

333

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Benchmarking the MBE, FMO, and CPF GPU-Accelerated Fragmentation Methods for Accuracy and Parallel Time-to-Solution

Fazeleh Kazemian, Jorge Galvez Vallejo, Andrew Gilbert, Zoe Seeger, Ekaterina Izgorodina, Giuseppe Maria Junior Barca

Version 1 posted 12 October 2023

220

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Theoretical and Computational Chemistry

Working Paper

VeloxChem: GPU-accelerated Fock matrix construction enabling complex polarization propagator simulations of circular dichroism spectra of G-quadruplexes

Xin Li, Mathieu Linares, Patrick Norman

Version 1 posted 05 November 2024

138

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Theoretical and Computational Chemistry

Working Paper

An Efficient RI-MP2 Algorithm for Distributed Many-GPU Architectures

Calum Snowdon, Giuseppe Maria Junior Barca

Version 2 posted 19 September 2024

94

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Theoretical and Computational Chemistry

Working Paper

High-performance multi-GPU analytic RI-MP2 energy gradients

Ryan Stocks, Elise Palethorpe, Giuseppe Maria Junior Barca

Version 1 posted 19 February 2024

302

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Biological and Medicinal Chemistry

Working Paper

Accelerating AutoDock VINA with GPUs

Tang Shidi, Chen Ruiqi, Lin Mengru, Lin Qingde, Zhu Yanxiang, Ding Ji, Wu Jiansheng, Hu Haifeng, Ling Ming

Version 4 posted 25 March 2022

3,098

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Theoretical and Computational Chemistry

Working Paper

Translating the Molecules: Adapting Neural Machine Translation to Predict IUPAC Names from a Chemical Identifier

Jennifer Handsel, Brian Matthews, Nicola Knight, Simon Coles

Version 1 posted 08 March 2021

567

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1

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Theoretical and Computational Chemistry

Working Paper

MDBenchmark: A Toolkit to Optimize the Performance of Molecular Dynamics Simulations

Michael Gecht, Marc Siggel, Max Linke, Gerhard Hummer, Juergen Koefinger

Version 2 posted 28 August 2020

1,291

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14 results in GPU in Keywords: GPU

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

A Fast Implementation of the Nudged Elastic Band Method in AMBER

TORO Indexer: A PyTorch-Based Indexing Algorithm for kHz Serial Crystallography

Benchmarking the MBE, FMO, and CPF GPU-Accelerated Fragmentation Methods for Accuracy and Parallel Time-to-Solution

VeloxChem: GPU-accelerated Fock matrix construction enabling complex polarization propagator simulations of circular dichroism spectra of G-quadruplexes

An Efficient RI-MP2 Algorithm for Distributed Many-GPU Architectures

High-performance multi-GPU analytic RI-MP2 energy gradients

Accelerating AutoDock VINA with GPUs

Translating the Molecules: Adapting Neural Machine Translation to Predict IUPAC Names from a Chemical Identifier

MDBenchmark: A Toolkit to Optimize the Performance of Molecular Dynamics Simulations

14 results in Keywords: GPU