Literature DB >> 21528950

Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle.

Ikuo Fukuda1, Yasushige Yonezawa, Haruki Nakamura.   

Abstract

We propose a novel idea, zero-dipole summation, for evaluating the electrostatic energy of a classical particle system, and have composed an algorithm for effectively utilizing the idea for molecular dynamics. It conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. The resulting energy formula is nevertheless represented by a simple pairwise function sum, which enables facile application to high-performance computation. By following a heuristic approach to derive the current electrostatic energy formula, we developed an axiomatic approach to construct the method consistently. Explorations of the theoretical details of our method revealed the structure of the generated error, and we analyzed it by comparisons with other methods. A numerical simulation using liquid sodium chloride confirmed that the current method with a small damping factor yielded sufficient accuracy with a practical cutoff distance region. The current energy function also conducts stable numerical integration in a liquid MD simulation. Our method is an extension of the charge neutralized summation developed by Wolf et al. [J. Chem. Phys. 110, 8254 (1999)]. Furthermore, we found that the current method becomes a generalization of the preaveraged potential method proposed by Yakub and Ronchi [J. Chem. Phys. 119, 11556 (2003)], which is based on a viewpoint different from the neutrality. The current study presents these relationships and suggests possibilities for their further applications.

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Year:  2011        PMID: 21528950     DOI: 10.1063/1.3582791

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  20 in total

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2.  Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level.

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Journal:  Methods Mol Biol       Date:  2021

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4.  Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism.

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Journal:  Protein Eng Des Sel       Date:  2019-12-31       Impact factor: 1.650

5.  Non-Ewald methods: theory and applications to molecular systems.

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Journal:  Biophys Rev       Date:  2012-08-02

6.  Sphingolipids with 2-hydroxy fatty acids aid in plasma membrane nanodomain organization and oxidative burst.

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7.  Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations.

Authors:  Pedro Ojeda-May; Jingzhi Pu
Journal:  J Chem Phys       Date:  2015-11-07       Impact factor: 3.488

8.  Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: theory, simulations, and experiments.

Authors:  Zaven Ovanesyan; Bharat Medasani; Marcia O Fenley; Guillermo Iván Guerrero-García; Mónica Olvera de la Cruz; Marcelo Marucho
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

9.  Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities.

Authors:  Tomonori Hayami; Narutoshi Kamiya; Kota Kasahara; Takeshi Kawabata; Jun-Ichi Kurita; Yoshifumi Fukunishi; Yoshifumi Nishimura; Haruki Nakamura; Junichi Higo
Journal:  Sci Rep       Date:  2021-03-17       Impact factor: 4.379

10.  Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations.

Authors:  Gert-Jan Bekker; Ikuo Fukuda; Junichi Higo; Yoshifumi Fukunishi; Narutoshi Kamiya
Journal:  Sci Rep       Date:  2021-03-03       Impact factor: 4.379

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