Literature DB >> 24206287

Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system.

Ikuo Fukuda1.   

Abstract

The zero-multipole summation method has been developed to efficiently evaluate the electrostatic Coulombic interactions of a point charge system. This summation prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large amounts of energetic noise and significant artifacts. The resulting energy function is represented by a constant term plus a simple pairwise summation, using a damped or undamped Coulombic pair potential function along with a polynomial of the distance between each particle pair. Thus, the implementation is straightforward and enables facile applications to high-performance computations. Any higher-order multipole moment can be taken into account in the neutrality principle, and it only affects the degree and coefficients of the polynomial and the constant term. The lowest and second moments correspond respectively to the Wolf zero-charge scheme and the zero-dipole summation scheme, which was previously proposed. Relationships with other non-Ewald methods are discussed, to validate the current method in their contexts. Good numerical efficiencies were easily obtained in the evaluation of Madelung constants of sodium chloride and cesium chloride crystals.

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Year:  2013        PMID: 24206287     DOI: 10.1063/1.4827055

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


  7 in total

Review 1.  Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.

Authors:  Jinzen Ikebe; Koji Umezawa; Junichi Higo
Journal:  Biophys Rev       Date:  2016-01-11

2.  myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.

Authors:  Kota Kasahara; Benson Ma; Kota Goto; Bhaskar Dasgupta; Junichi Higo; Ikuo Fukuda; Tadaaki Mashimo; Yutaka Akiyama; Haruki Nakamura
Journal:  Biophys Physicobiol       Date:  2016-09-07

3.  Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer.

Authors:  Kota Kasahara; Masaaki Shiina; Ikuo Fukuda; Kazuhiro Ogata; Haruki Nakamura
Journal:  PLoS One       Date:  2017-02-23       Impact factor: 3.240

4.  Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.

Authors:  Kota Kasahara; Masaaki Shiina; Junichi Higo; Kazuhiro Ogata; Haruki Nakamura
Journal:  Nucleic Acids Res       Date:  2018-03-16       Impact factor: 16.971

Review 5.  Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review.

Authors:  Kota Kasahara; Hiroki Terazawa; Takuya Takahashi; Junichi Higo
Journal:  Comput Struct Biotechnol J       Date:  2019-06-13       Impact factor: 7.271

6.  Generalized Moment Correction for Long-Ranged Electrostatics.

Authors:  Björn Stenqvist; Vidar Aspelin; Mikael Lund
Journal:  J Chem Theory Comput       Date:  2020-05-07       Impact factor: 6.006

7.  Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations.

Authors:  Narutoshi Kamiya; Tadaaki Mashimo; Yu Takano; Takahide Kon; Genji Kurisu; Haruki Nakamura
Journal:  Protein Eng Des Sel       Date:  2016-06-21       Impact factor: 1.650

  7 in total

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