Literature DB >> 27317328

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

Hiroaki Nishizawa1, Yoshifumi Nishimura1,2, Masato Kobayashi3,4,5, Stephan Irle6, Hiromi Nakai2,4,7,8.   

Abstract

The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer.
© 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Entities:  

Keywords:  density-functional tight-binding method; linear-scaling divide-and-conquer method; massively parallel computation; quantum mechanical molecular dynamics

Year:  2016        PMID: 27317328     DOI: 10.1002/jcc.24419

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  8 in total

1.  Quantum mechanical force fields for condensed phase molecular simulations.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Phys Condens Matter       Date:  2017-08-17       Impact factor: 2.333

2.  Simulations of the synthesis of boron-nitride nanostructures in a hot, high pressure gas volume.

Authors:  Predrag S Krstic; Longtao Han; Stephan Irle; Hiromi Nakai
Journal:  Chem Sci       Date:  2018-03-19       Impact factor: 9.825

Review 3.  Quantum-Chemical Insights into the Self-Assembly of Carbon-Based Supramolecular Complexes.

Authors:  Joaquín Calbo; Juan Carlos Sancho-García; Enrique Ortí; Juan Aragó
Journal:  Molecules       Date:  2018-01-07       Impact factor: 4.411

4.  Reversible Sodium Metal Electrodes: Is Fluorine an Essential Interphasial Component?

Authors:  Kyosuke Doi; Yuki Yamada; Masaki Okoshi; Junichi Ono; Chien-Pin Chou; Hiromi Nakai; Atsuo Yamada
Journal:  Angew Chem Int Ed Engl       Date:  2019-05-14       Impact factor: 15.336

Review 5.  Perspectives in the Computational Modeling of New Generation, Biocompatible Ionic Liquids.

Authors:  Enrico Bodo
Journal:  J Phys Chem B       Date:  2022-01-03       Impact factor: 2.991

Review 6.  Computational and data driven molecular material design assisted by low scaling quantum mechanics calculations and machine learning.

Authors:  Wei Li; Haibo Ma; Shuhua Li; Jing Ma
Journal:  Chem Sci       Date:  2021-11-08       Impact factor: 9.825

7.  Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations.

Authors:  Junichi Ono; Uika Koshimizu; Yoshifumi Fukunishi; Hiromi Nakai
Journal:  Chem Phys Lett       Date:  2022-02-22       Impact factor: 2.328

8.  Density-functional tight-binding: basic concepts and applications to molecules and clusters.

Authors:  Fernand Spiegelman; Nathalie Tarrat; Jérôme Cuny; Leo Dontot; Evgeny Posenitskiy; Carles Martí; Aude Simon; Mathias Rapacioli
Journal:  Adv Phys X       Date:  2020-02-18
  8 in total

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