Literature DB >> 26620654

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation.

Ivan S Ufimtsev1, Todd J Martínez1.   

Abstract

Modern videogames place increasing demands on the computational and graphical hardware, leading to novel architectures that have great potential in the context of high performance computing and molecular simulation. We demonstrate that Graphical Processing Units (GPUs) can be used very efficiently to calculate two-electron repulsion integrals over Gaussian basis functions [Formula: see text] the first step in most quantum chemistry calculations. A benchmark test performed for the evaluation of approximately 10(6) (ss|ss) integrals over contracted s-orbitals showed that a naïve algorithm implemented on the GPU achieves up to 130-fold speedup over a traditional CPU implementation on an AMD Opteron. Subsequent calculations of the Coulomb operator for a 256-atom DNA strand show that the GPU advantage is maintained for basis sets including higher angular momentum functions.

Entities:  

Year:  2008        PMID: 26620654     DOI: 10.1021/ct700268q

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  38 in total

1.  Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units.

Authors:  Ramu Anandakrishnan; Tom R W Scogland; Andrew T Fenley; John C Gordon; Wu-chun Feng; Alexey V Onufriev
Journal:  J Mol Graph Model       Date:  2010-06       Impact factor: 2.518

2.  Molecular simulation methods in drug discovery: a prospective outlook.

Authors:  Xavier Barril; F Javier Luque
Journal:  J Comput Aided Mol Des       Date:  2011-12-08       Impact factor: 3.686

3.  GPU-accelerated molecular modeling coming of age.

Authors:  John E Stone; David J Hardy; Ivan S Ufimtsev; Klaus Schulten
Journal:  J Mol Graph Model       Date:  2010-07-08       Impact factor: 2.518

4.  Hybrid dynamics simulation engine for metalloproteins.

Authors:  Manuel Sparta; David Shirvanyants; Feng Ding; Nikolay V Dokholyan; Anastassia N Alexandrova
Journal:  Biophys J       Date:  2012-08-22       Impact factor: 4.033

5.  Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units.

Authors:  Ruxi Qi; Ray Luo
Journal:  J Chem Inf Model       Date:  2018-12-31       Impact factor: 4.956

6.  Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation.

Authors:  Zhongyue Yang; Rimsha Mehmood; Mengyi Wang; Helena W Qi; Adam H Steeves; Heather J Kulik
Journal:  React Chem Eng       Date:  2018-11-29       Impact factor: 4.239

7.  TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units.

Authors:  Stefan Seritan; Christoph Bannwarth; B Scott Fales; Edward G Hohenstein; Sara I L Kokkila-Schumacher; Nathan Luehr; James W Snyder; Chenchen Song; Alexey V Titov; Ivan S Ufimtsev; Todd J Martínez
Journal:  J Chem Phys       Date:  2020-06-14       Impact factor: 3.488

8.  Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer.

Authors:  Heather J Kulik
Journal:  Phys Chem Chem Phys       Date:  2018-08-08       Impact factor: 3.676

9.  Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units.

Authors:  Ruxi Qi; Wesley M Botello-Smith; Ray Luo
Journal:  J Chem Theory Comput       Date:  2017-06-07       Impact factor: 6.006

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

Authors:  Christine M Isborn; Andreas W Götz; Matthew A Clark; Ross C Walker; Todd J Martínez
Journal:  J Chem Theory Comput       Date:  2012-10-06       Impact factor: 6.006

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