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

• 資料種別: 記事
• タイトル: Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system
• 著者標目: Fukuda, Ikuo
• 出版年月日等: 2013
• 出版年（W3CDTF）: 2013
• タイトル（掲載誌）: The Journal of Chemical Physics
• 巻号年月日等（掲載誌）: 139
• 掲載巻: 139
• 掲載ページ: 174107-
• 掲載年月日（W3CDTF）: 2013
• ISSN（掲載誌）: 00219606
• 出版事項（掲載誌）: AIP Publishing
• 本文の言語コード: en
• 件名標目: Chlorides; Static Electricity; Cesium; Molecular Dynamics Simulation; Sodium Chloride; Monte Carlo Method
• 対象利用者: 一般
• 標準番号（その他）: PMID : 24206287
• DOI: 10.1063/1.4827055
• オンライン閲覧公開範囲: インターネット公開
• 著作権情報: Copyright (2013) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.
• 関連情報（URI）: https://hdl.handle.net/11094/52403; https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/1.4827055/15466888/174107_1_online.pdf
• 参照: The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics : Analysis of the accuracy and application to liquid systems; https://cir.nii.ac.jp/crid/1050299693926776320; Performance evaluation of the zero‐multipole summation method in modern molecular dynamics software; https://cir.nii.ac.jp/crid/1360004230163485952; Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations; https://cir.nii.ac.jp/crid/1360005745358624640; Revisiting antibody modeling assessment for CDR-H3 loop; https://cir.nii.ac.jp/crid/1360283692630498304; Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer; https://cir.nii.ac.jp/crid/1360285712581435008; Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference; https://cir.nii.ac.jp/crid/1360298757428021760; A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems; https://cir.nii.ac.jp/crid/1360302865536745856; A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system; https://cir.nii.ac.jp/crid/1360565167058212224; TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of Proteins; https://cir.nii.ac.jp/crid/1360567183082170368; Enhanced sampling simulations to construct free-energy landscape of protein–partner substrate interaction; https://cir.nii.ac.jp/crid/1360848656471911552; Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation; https://cir.nii.ac.jp/crid/1360848658063310208; Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state; https://cir.nii.ac.jp/crid/1360848659601997824; Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations; https://cir.nii.ac.jp/crid/1360848659673731328; Fast multipole method for three‐dimensional systems with periodic boundary condition in two directions; https://cir.nii.ac.jp/crid/1360849939667082752; Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review; https://cir.nii.ac.jp/crid/1361975841618698112; myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme; https://cir.nii.ac.jp/crid/1390282680741170688; 分子動力学計算における新規非エバルト法の開発と応用; https://cir.nii.ac.jp/crid/1390282681512737152; 味覚受容体タンパクとリガンドの相互作用に関する分子動力学シミュレーション; https://cir.nii.ac.jp/crid/1390577232659111424
• 参照: Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle; https://cir.nii.ac.jp/crid/1050018218949968256; Simple and accurate scheme to compute electrostatic interaction : Zero-dipole summation technique for molecular system and application to bulk water; https://cir.nii.ac.jp/crid/1050581168903390592; Computer simulation of charged hard spherocylinders at low temperatures; https://cir.nii.ac.jp/crid/1360011144438410624; Isotropic periodic sum of electrostatic interactions for polar systems; https://cir.nii.ac.jp/crid/1360011144640551680; Monte Carlo studies of the dielectric properties of water-like models; https://cir.nii.ac.jp/crid/1360011146173686400; Monte Carlo Study of a One-Component Plasma. I; https://cir.nii.ac.jp/crid/1360292619310487424; Surface effects on the piezoelectricity of ZnO nanowires; https://cir.nii.ac.jp/crid/1360292620363947264; MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES: Long-Range Electrostatic Effects; https://cir.nii.ac.jp/crid/1360292620848171520; Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r−1 summation; https://cir.nii.ac.jp/crid/1360292620891867392; Vibrational Sum-Frequency Generation Spectroscopy at the Water/Lipid Interface: Molecular Dynamics Simulation Study; https://cir.nii.ac.jp/crid/1360292621538460672; A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics; https://cir.nii.ac.jp/crid/1360567183850576256; Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method; https://cir.nii.ac.jp/crid/1360574094123478784; Reconstruction of NaCl surfaces from a dipolar solution to the Madelung problem; https://cir.nii.ac.jp/crid/1360574094784710400; A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics; https://cir.nii.ac.jp/crid/1360574096252218624; Non-Ewald methods: theory and applications to molecular systems; https://cir.nii.ac.jp/crid/1360848656471852672; Application of zero-dipole summation method to molecular dynamics simulations of a membrane protein system; https://cir.nii.ac.jp/crid/1360848657014691840; Computer simulation of sedimentation of ionic systems using the Wolf method; https://cir.nii.ac.jp/crid/1360855570713450880; Molecular dynamics studies of ultrafast laser-induced nonthermal melting; https://cir.nii.ac.jp/crid/1360855570967859584; Monte Carlo simulations of primitive models for ionic systems using the Wolf method; https://cir.nii.ac.jp/crid/1361137043790287104; An efficient method for computation of long-ranged Coulomb forces in computer simulation of ionic fluids; https://cir.nii.ac.jp/crid/1361137043888007680; Coulomb interactions in charged fluids; https://cir.nii.ac.jp/crid/1361137044648273152; Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics; https://cir.nii.ac.jp/crid/1361137045310794240; The Origin of Layer Structure Artifacts in Simulations of Liquid Water; https://cir.nii.ac.jp/crid/1361137046323256576; Screening, charge distribution, and electron correlations in metallic alloys; https://cir.nii.ac.jp/crid/1361418520420178176; Potential of mean force between identical charged nanoparticles immersed in a size-asymmetric monovalent electrolyte; https://cir.nii.ac.jp/crid/1361418521067068800; New applications of Poisson's summation formula; https://cir.nii.ac.jp/crid/1361418521178818432; Simple calculation of Madelung constants; https://cir.nii.ac.jp/crid/1361699993508197632; Isotropic periodic sum: A method for the calculation of long-range interactions; https://cir.nii.ac.jp/crid/1361699994828748544; A gentler approach to RNEMD: Nonisotropic velocity scaling for computing thermal conductivity and shear viscosity; https://cir.nii.ac.jp/crid/1361699995118418048; Adsorption and Diffusion of Small Alcohols in Zeolitic Imidazolate Frameworks ZIF-8 and ZIF-90; https://cir.nii.ac.jp/crid/1361699995535697280; The potential within a crystal lattice; https://cir.nii.ac.jp/crid/1361699995551193216; Corner ion, edge-center ion, and face-center ion Madelung expressions for sodium chloride; https://cir.nii.ac.jp/crid/1361699995901538304; Comparison of the Ewald and Wolf methods for modeling electrostatic interactions in nanowires; https://cir.nii.ac.jp/crid/1361981468522218496; Reaction field simulation of water; https://cir.nii.ac.jp/crid/1361981469144200704; Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation; https://cir.nii.ac.jp/crid/1362262943417705472; Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants; https://cir.nii.ac.jp/crid/1362262943590835584; Convergence analysis of the Wolf method for Coulombic interactions; https://cir.nii.ac.jp/crid/1362262944732644352; Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural, and dielectric properties of liquid water; https://cir.nii.ac.jp/crid/1362262944784634240; Carrier transport simulation of anomalous temperature dependence in nematic liquid crystals; https://cir.nii.ac.jp/crid/1362262945023401472; High frequency sound velocity in the glass former<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mn>2</mml:mn><mml:mi mathvariant="normal">Ca</mml:mi><mml:msub><mml:mrow><mml:mo>(</mml:mo><mml:mi mathvariant="normal">N</mml:mi><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn>3</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:msub><mml:mo>∙</mml:mo><mml:mn>3</mml:mn><mml:mi mathvariant="normal">K</mml:mi><mml:mi mathvariant="normal">N</mml:mi><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:mrow></mml:math>: Molecular dynamics simulations; https://cir.nii.ac.jp/crid/1362262945810001664; New spherical‐cutoff methods for long‐range forces in macromolecular simulation; https://cir.nii.ac.jp/crid/1362262946325904896; Summation of Coulomb fields in computer-simulated disordered systems; https://cir.nii.ac.jp/crid/1362544418396551680; Electronic-Structure Studies of Solids. I. Fourier Representation Method for Madelung Sums; https://cir.nii.ac.jp/crid/1362544421009478656; Effects of edge dislocations on thermal transport in UO2; https://cir.nii.ac.jp/crid/1362544421104079872; Interface Effects in Ferroelectric<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi>PbTiO</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:math>Ultrathin Films on a Paraelectric Substrate; https://cir.nii.ac.jp/crid/1362825893706277632; A New Method for Computation of Long Ranged Coulomb Forces in Computer Simulation of Disordered Systems; https://cir.nii.ac.jp/crid/1362825894067363456; Effective way to sum over long-range Coulomb potentials in two and three dimensions; https://cir.nii.ac.jp/crid/1362825894094575232; Solute and Solvent Dynamics in Confined Equal-Sized Aqueous Environments of Charged and Neutral Reverse Micelles: A Combined Dynamic Fluorescence and All-Atom Molecular Dynamics Simulation Study; https://cir.nii.ac.jp/crid/1362825894920344704; Molecular dynamics simulation of highly charged proteins: Comparison of the particle‐particle particle‐mesh and reaction field methods for the calculation of electrostatic interactions; https://cir.nii.ac.jp/crid/1362825895774899456; Convergence of lattice sums and Madelung’s constant; https://cir.nii.ac.jp/crid/1363107369014974208; Madelung Constants of Simple Crystals Expressed in Terms of Born's Basic Potentials of 15 Figures; https://cir.nii.ac.jp/crid/1363107370428314496; Semi-ab initio interionic potential for gadolinia-doped ceria; https://cir.nii.ac.jp/crid/1363388844158886400; Atomic Charges Derived from Electrostatic Potentials for Molecular and Periodic Systems; https://cir.nii.ac.jp/crid/1363388844199726208; Effective computer simulation of strongly coupled Coulomb fluids; https://cir.nii.ac.jp/crid/1363388844217159424; Effects of long‐range electrostatic forces on simulated protein folding kinetics; https://cir.nii.ac.jp/crid/1363388844399839488; An Alternative to Ewald Sums, Part 2: The Coulomb Potential in a Periodic System; https://cir.nii.ac.jp/crid/1363388845002532096; New Representations for the Madelung Constant; https://cir.nii.ac.jp/crid/1363670318609808000; Madelung energy of the valence-skipping compound<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi mathvariant="normal">Ba</mml:mi><mml:mi mathvariant="normal">Bi</mml:mi><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:mrow></mml:math>; https://cir.nii.ac.jp/crid/1363670318819216640; Correct virial formulation in the isotropic periodic sum method; https://cir.nii.ac.jp/crid/1363670320078399104; Removing systematic errors in interionic potentials of mean force computed in molecular simulations using reaction-field-based electrostatics; https://cir.nii.ac.jp/crid/1363670320111687424; Electric Moments of Molecules in Liquids; https://cir.nii.ac.jp/crid/1363951793506889600; Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems; https://cir.nii.ac.jp/crid/1363951793629737856; Accurate calculation of Coulomb sums: Efficacy of Padé-like methods; https://cir.nii.ac.jp/crid/1363951794159891456; Molecular dynamics study of screening at ionic surfaces; https://cir.nii.ac.jp/crid/1364233268328861824; Development of the CHARMM Force Field for Lipids; https://cir.nii.ac.jp/crid/1364233268394762880; Unit cell for a lattice electrostatic potential; https://cir.nii.ac.jp/crid/1364233269319690240; Dissociative Water Potential for Molecular Dynamics Simulations; https://cir.nii.ac.jp/crid/1364233269911896704; Concurrent atomistic and continuum simulation of strontium titanate; https://cir.nii.ac.jp/crid/1364233270001715072; Kinetically evolving irradiation-induced point defect clusters in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mtext>UO</mml:mtext></mml:mrow><mml:mn>2</mml:mn></mml:msub></mml:mrow></mml:math>by molecular dynamics simulation; https://cir.nii.ac.jp/crid/1364233270842286848; Consistent Molecular Dynamics Scheme Applying the Wolf Summation for Calculating Electrostatic Interaction of Particles; https://cir.nii.ac.jp/crid/1390001204198027520; New Series Representation for the Madelung Constant; https://cir.nii.ac.jp/crid/1523669555313506176
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• 要約等: The following article appeared in J. Chem. Phys. 139, 174107 (2013) and may be found at http://scitation.aip.org/content/aip/journal/jcp/139/17/10.106...