Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model

Hideo Doi; Tatsuya Nakano; Kota Sakakura; Kazuki Akisawa; Koji Okuwaki; Yoshinori Hirano; Eiji Yamamoto; Kenji Yasuoka; Satoshi Ohshima; Takahiro Katagiri; Yuji Mochizuki

doi:10.1002/jcc.70052

Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model

Hideo Doi
, Tatsuya Nakano
, Kota Sakakura
, Kazuki Akisawa
, Koji Okuwaki
, Yoshinori Hirano
, Eiji Yamamoto
, Kenji Yasuoka
, Satoshi Ohshima
, Takahiro Katagiri
, Yuji Mochizuki

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

Abstract

The spike protein of SARS-CoV-2 is a challenging target for theoretical approaches. Here we report a benchmark calculation of the spike protein droplet model by the fragment molecular orbital (FMO) at the second-order Møller-Plesset perturbation (MP2) level on the supercomputer Fugaku. One hundred structure samples from molecular dynamics (MD) simulations were used for both the closed and open forms of this protein (PDB IDs 6XLU and 6XM0 respectively). The number of total fragments is about 20,000, and the job time per structure was about 2 h on 8 racks of Fugaku.

Original language	English
Article number	e70052
Journal	Journal of Computational Chemistry
Volume	46
Issue number	4
DOIs	https://doi.org/10.1002/jcc.70052
Publication status	Published - 2025 Feb 5

Keywords

FMO
MP2
droplet model
fragment molecular orbital method
second-order Møller-Plesset perturbation
spike protein
supercomputer Fugaku

ASJC Scopus subject areas

General Chemistry
Computational Mathematics

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10.1002/jcc.70052

Cite this

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title = "Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model",

abstract = "The spike protein of SARS-CoV-2 is a challenging target for theoretical approaches. Here we report a benchmark calculation of the spike protein droplet model by the fragment molecular orbital (FMO) at the second-order M{\o}ller-Plesset perturbation (MP2) level on the supercomputer Fugaku. One hundred structure samples from molecular dynamics (MD) simulations were used for both the closed and open forms of this protein (PDB IDs 6XLU and 6XM0 respectively). The number of total fragments is about 20,000, and the job time per structure was about 2 h on 8 racks of Fugaku.",

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AU - Doi, Hideo

AU - Nakano, Tatsuya

AU - Sakakura, Kota

AU - Akisawa, Kazuki

AU - Okuwaki, Koji

AU - Hirano, Yoshinori

AU - Yamamoto, Eiji

AU - Yasuoka, Kenji

AU - Ohshima, Satoshi

AU - Katagiri, Takahiro

AU - Mochizuki, Yuji

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AB - The spike protein of SARS-CoV-2 is a challenging target for theoretical approaches. Here we report a benchmark calculation of the spike protein droplet model by the fragment molecular orbital (FMO) at the second-order Møller-Plesset perturbation (MP2) level on the supercomputer Fugaku. One hundred structure samples from molecular dynamics (MD) simulations were used for both the closed and open forms of this protein (PDB IDs 6XLU and 6XM0 respectively). The number of total fragments is about 20,000, and the job time per structure was about 2 h on 8 racks of Fugaku.

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KW - droplet model

KW - fragment molecular orbital method

KW - second-order Møller-Plesset perturbation

KW - spike protein

KW - supercomputer Fugaku

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Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model

Abstract

Keywords

ASJC Scopus subject areas

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