Article

Full Electron Calculation Beyond 20,000 Atoms: Ground Electronic State of Photosynthetic Proteins

Authors:

TSUTOMU IKEGAMI,

TOYOKAZU ISHIDA,

DMITRI G. FEDOROV,

YUICHI INADOMI,

MITSUO YOKOKAWA,

SATOSHI SEKIGUCHIAuthors Info & Claims

SC '05: Proceedings of the 2005 ACM/IEEE conference on Supercomputing

Page 10

https://doi.org/10.1109/SC.2005.28

Published: 12 November 2005 Publication History

Abstract

A full electron calculation for the photosynthetic reaction center of Rhodopseudomonas viridis was performed by using the fragment molecular orbital (FMO) method on a massive cluster computer. The target system contains 20,581 atoms and 77,754 electrons, which was divided into 1,398 fragments. According to the FMO prescription, the calculations of the fragments and pairs of the fragments were conducted to obtain the electronic state of the system. The calculation at RHF/6-31G* level of theory took 72.5 hours with 600 CPUs. The CPUs were grouped into several workers, to which the calculations of the fragments were dispatched. An uneven CPU grouping, where two types of workers are generated, was shown to be efficient.

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Cited By

Nomura KKalia RNakano AVashishta PShimamura KShimojo FKunaseth MMessina PRomero NDamkroger TDongarra J(2014)Metascalable quantum molecular dynamics simulations of hydrogen-on-demandProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1109/SC.2014.59(661-673)Online publication date: 16-Nov-2014
https://dl.acm.org/doi/10.1109/SC.2014.59
Alexeev YMahajan ALeyffer SFletcher GFedorov DHollingsworth J(2012)Heuristic static load-balancing algorithm applied to the fragment molecular orbital methodProceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis10.5555/2388996.2389072(1-13)Online publication date: 10-Nov-2012
https://dl.acm.org/doi/10.5555/2388996.2389072
Nakano AKalia RNomura KSharma AVashishta PShimojo FC. T. Van Duin AGoddard WBiswas RSrivastava DYang L(2008)De Novo Ultrascale Atomistic Simulations On High-End Parallel SupercomputersInternational Journal of High Performance Computing Applications10.1177/109434200708501522:1(113-128)Online publication date: 1-Feb-2008
https://dl.acm.org/doi/10.1177/1094342007085015
Show More Cited By

Index Terms

Full Electron Calculation Beyond 20,000 Atoms: Ground Electronic State of Photosynthetic Proteins

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Published In

cover image ACM Conferences

SC '05: Proceedings of the 2005 ACM/IEEE conference on Supercomputing

November 2005

829 pages

ISBN:1595930612

General Chair:
William Kramer

Sponsors

SIGARCH: ACM Special Interest Group on Computer Architecture
IEEE-CS: Computer Society

Publisher

IEEE Computer Society

United States

Publication History

Published: 12 November 2005

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SC '05

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SIGARCH
IEEE-CS

SC '05: International Conference for High Performance Computing, Networking, Storage and Analysis

November 12 - 18, 2005

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SC '05 Paper Acceptance Rate 62 of 260 submissions, 24%;

Overall Acceptance Rate 1,516 of 6,373 submissions, 24%

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Cited By

Nomura KKalia RNakano AVashishta PShimamura KShimojo FKunaseth MMessina PRomero NDamkroger TDongarra J(2014)Metascalable quantum molecular dynamics simulations of hydrogen-on-demandProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1109/SC.2014.59(661-673)Online publication date: 16-Nov-2014
https://dl.acm.org/doi/10.1109/SC.2014.59
Alexeev YMahajan ALeyffer SFletcher GFedorov DHollingsworth J(2012)Heuristic static load-balancing algorithm applied to the fragment molecular orbital methodProceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis10.5555/2388996.2389072(1-13)Online publication date: 10-Nov-2012
https://dl.acm.org/doi/10.5555/2388996.2389072
Nakano AKalia RNomura KSharma AVashishta PShimojo FC. T. Van Duin AGoddard WBiswas RSrivastava DYang L(2008)De Novo Ultrascale Atomistic Simulations On High-End Parallel SupercomputersInternational Journal of High Performance Computing Applications10.1177/109434200708501522:1(113-128)Online publication date: 1-Feb-2008
https://dl.acm.org/doi/10.1177/1094342007085015
Ikegamial TMaki JTakami TTanaka YYokokawa MSekiguchi SAoyagi M(2007)GridFMO Quantum chemistry of proteins on the gridProceedings of the 8th IEEE/ACM International Conference on Grid Computing10.1109/GRID.2007.4354128(153-160)Online publication date: 19-Sep-2007
https://dl.acm.org/doi/10.1109/GRID.2007.4354128
Takemiya HTanaka YSekiguchi SOgata SKalia RNakano AVashishta PHorner-Miller B(2006)Sustainable adaptive grid supercomputingProceedings of the 2006 ACM/IEEE conference on Supercomputing10.1145/1188455.1188566(106-es)Online publication date: 11-Nov-2006
https://dl.acm.org/doi/10.1145/1188455.1188566

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