Literature DB >> 26609609

Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation.

Ivan S Ufimtsev1, Todd J Martinez1.   

Abstract

We demonstrate the use of graphical processing units (GPUs) to carry out complete self-consistent-field calculations for molecules with as many as 453 atoms (2131 basis functions). Speedups ranging from 28× to 650× are achieved as compared to a mature third-party quantum chemistry program (GAMESS) running on a traditional CPU. The computational organization used to construct the Coulomb and exchange operators is discussed. We also present results using three GPUs in parallel, combining coarse and fine-grained parallelism.

Year:  2009        PMID: 26609609     DOI: 10.1021/ct800526s

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


  37 in total

1.  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

2.  Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

Authors:  Jonah Z Vilseck; Jakub Kostal; Julian Tirado-Rives; William L Jorgensen
Journal:  J Comput Chem       Date:  2015-08-27       Impact factor: 3.376

3.  An extensible interface for QM/MM molecular dynamics simulations with AMBER.

Authors:  Andreas W Götz; Matthew A Clark; Ross C Walker
Journal:  J Comput Chem       Date:  2013-10-09       Impact factor: 3.376

4.  Iterative stochastic subspace self-consistent field method.

Authors:  Pierre-François Loos; Jean-Louis Rivail; Xavier Assfeld
Journal:  J Mol Model       Date:  2017-05-02       Impact factor: 1.810

5.  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

6.  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

7.  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

8.  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

9.  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

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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