Literature DB >> 26631777

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics.

Ivan S Ufimtsev1, Todd J Martinez1.   

Abstract

We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree-Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born-Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.

Entities:  

Year:  2009        PMID: 26631777     DOI: 10.1021/ct9003004

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


  84 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.  Protonated Hexaazamacrocycles as Selective K(+) Receptors.

Authors:  Caterina Fraschetti; Antonello Filippi; Maria Elisa Crestoni; Enrico Marcantoni; Marco Glucini; Laura Guarcini; Maria Montagna; Leonardo Guidoni; Maurizio Speranza
Journal:  J Am Soc Mass Spectrom       Date:  2015-04-09       Impact factor: 3.109

3.  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

4.  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

5.  Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site.

Authors:  Lu Wang; Stephen D Fried; Steven G Boxer; Thomas E Markland
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-12       Impact factor: 11.205

6.  Driving torsion scans with wavefront propagation.

Authors:  Yudong Qiu; Daniel G A Smith; Chaya D Stern; Mudong Feng; Hyesu Jang; Lee-Ping Wang
Journal:  J Chem Phys       Date:  2020-06-28       Impact factor: 3.488

7.  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

8.  Q|R: quantum-based refinement.

Authors:  Min Zheng; Jeffrey R Reimers; Mark P Waller; Pavel V Afonine
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-01-01       Impact factor: 7.652

9.  Hole Hopping Across a Protein-Protein Interface.

Authors:  Kana Takematsu; Petr Pospíšil; Martin Pižl; Michael Towrie; Jan Heyda; Stanislav Záliš; Jens T Kaiser; Jay R Winkler; Harry B Gray; Antonín Vlček
Journal:  J Phys Chem B       Date:  2019-02-06       Impact factor: 2.991

10.  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

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