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Higher-order correlated calculations based on fragment molecular orbital scheme

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Abstract

We have developed a new module for higher-order correlated methods up to coupled-cluster singles and doubles with perturbative triples (CCSD(T)). The matrix-matrix operations through the DGEMM routine were pursued for a number of contractions. This code was then incorporated into the ABINIT-MPX program for the fragment molecular orbital (FMO) calculations. Intra-fragment processings were parallelized with OpenMP in a node-wise fashion, whereas the message passing interface (MPI) was used for the fragment-wise parallelization over nodes. Our new implementation made the FMO-based higher-order calculations applicable to realistic proteins. We have performed several benchmark tests on the Earth Simulator (ES2), a massively parallel computer. For example, the FMO-CCSD(T)/6-31G job for the HIV-1 protease (198 amino acid residues)–lopinavir complex was completed in 9.8 h with 512 processors (or 64 nodes). Another example was the influenza neuraminidase (386 residues) with oseltamivir calculated at the full fourth-order Møller–Plesset perturbation level (MP4), of which job timing was 10.3 h with 1024 processors. The applicability of the methods to commodity cluster computers was tested as well.

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Notes

  1. http://www.jamstec.go.jp/es/en/.

  2. http://www.netlib.org/blas/.

  3. http://www.mpi-forum.org/.

  4. http://www.openmp.org/.

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Acknowledgments

This work was supported by the CREST project operated by the Japan Science and Technology Agency (JST) and also by a Grant-in-Aid for Scientific Research on Priority Area "Molecular Theory for Real Systems" from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT). YM and TN are indebted for various supports by the RISS project at the Institute of Industrial Science (IIS) of the University of Tokyo. YM acknowledges the SFR-aid by Rikkyo University as well. Computing resource for all the calculations on the Earth Simulator (ES2) was supplied by the Japan Agency for Marine-Earth Science and Technology (JAMSTEC). The authors thank Dr. Yuto Komeiji for critical comments on the manuscript. Finally, YM is grateful to the late Dr. Hideki Katagiri, who passed away in December 2010, for stimulating discussions on CC theories at the early stage of this work.

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Authors and Affiliations

  1. Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan

    Yuji Mochizuki & Naoki Taguchi

  2. Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan

    Yuji Mochizuki, Tatsuya Nakano, Yoshio Okiyama & Kaori Fukuzawa

  3. CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan

    Yuji Mochizuki, Tatsuya Nakano & Shigenori Tanaka

  4. 1st Manufacturing Industries Solutions Division, NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo, 136-8608, Japan

    Katsumi Yamashita

  5. Division of Medicinal Safety Science, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan

    Tatsuya Nakano

  6. Mizuho Information and Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo, 101-8443, Japan

    Kaori Fukuzawa

  7. Graduate School of System Informatics, Department of Computational Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan

    Shigenori Tanaka

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  1. Yuji Mochizuki
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  2. Katsumi Yamashita
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Correspondence to Yuji Mochizuki.

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Dedicated to Professor Shigeru Nagase on the occasion of his 65th birthday and published as part of the Nagase Festschrift Issue.

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Mochizuki, Y., Yamashita, K., Nakano, T. et al. Higher-order correlated calculations based on fragment molecular orbital scheme. Theor Chem Acc 130, 515–530 (2011). https://doi.org/10.1007/s00214-011-1036-3

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