ようこそ ゲスト さん
雑誌ブラウズ
雑誌 全て
大阪大学 刊行物
ランキング
アクセスランキング
ダウンロードランキング
博士論文のみをさがす
このアイテムのアクセス数:
101
件
（
2018-08-21
01:25 集計
）
このアイテムへのリンクには次のURLをご利用ください:http://hdl.handle.net/11094/52401
閲覧可能ファイル
ファイル
フォーマット
サイズ
閲覧回数
説明
SupplementaryMaterial_J
pdf
50.9 KB
21
J
pdf
1.94 MB
40
出版社版/publisher
論文情報
タイトル
Simple and accurate scheme to compute electrostatic interaction : Zero-dipole summation technique for molecular system and application to bulk water
著者
Kamiya, Narutoshi
Kamiya, Narutoshi
Yonezawa, Yasushige
Yonezawa, Yasushige
Nakamura, Haruki
Nakamura, Haruki
Fukuda, Ikuo
Fukuda, Ikuo
内容
The following article appeared in J. Chem. Phys. 137, 054314 (2012) and may be found at http://scitation.aip.org/content/aip/journal/jcp/137/5/10.1063/1.4739789
抄録
The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys.134, 164107 (2011)10.1063/1.3582791], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a cutoff length longer than 13 Å for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical cutoff distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we treated. We discussed the origin of this difference between the two schemes and the dependence of this fact on the physical system. The use of the zero damping-factor will enhance the efficiency of practical computations, since the complementary error function is not employed. In addition, utilizing the zero damping-factor provides freedom from the parameter choice, which is not trivial in the zero-charge scheme, and eliminates the error function term, which corresponds to the time-consuming Fourier part under the periodic boundary conditions.
公開者
AIP Publishing
掲載誌名
The Journal of Chemical Physics
巻
137
開始ページ
054314
刊行年月
2012
ISSN
00219606
10897690
URL
http://hdl.handle.net/11094/52401
権利情報
Copyright (2012) 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.
言語
英語
論文詳細を表示
著者版フラグ
publisher
NII資源タイプ
学術雑誌論文
ローカル資源タイプ
学術雑誌論文
dcmi資源タイプ
text
DCTERMS.bibliographicCitation
The Journal of Chemical Physics.137 P.054314
DC.title
Simple and accurate scheme to compute electrostatic interaction : Zero-dipole summation technique for molecular system and application to bulk water
DC.creator
Kamiya, Narutoshi
Yonezawa, Yasushige
Nakamura, Haruki
Fukuda, Ikuo
DC.publisher
AIP Publishing
DC.language" scheme="DCTERMS.RFC1766
英語
DCTERMS.issued" scheme="DCTERMS.W3CDTF
2012
DC.identifier" scheme="DCTERMS.URI
http://hdl.handle.net/11094/52401
DC.description
The following article appeared in J. Chem. Phys. 137, 054314 (2012) and may be found at http://scitation.aip.org/content/aip/journal/jcp/137/5/10.1063/1.4739789
DCTERMS.abstract
The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys.134, 164107 (2011)10.1063/1.3582791], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a cutoff length longer than 13 Å for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical cutoff distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we treated. We discussed the origin of this difference between the two schemes and the dependence of this fact on the physical system. The use of the zero damping-factor will enhance the efficiency of practical computations, since the complementary error function is not employed. In addition, utilizing the zero damping-factor provides freedom from the parameter choice, which is not trivial in the zero-charge scheme, and eliminates the error function term, which corresponds to the time-consuming Fourier part under the periodic boundary conditions.
DC.rights
Copyright (2012) 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.
citation_title
Simple and accurate scheme to compute electrostatic interaction : Zero-dipole summation technique for molecular system and application to bulk water
citation_author
Kamiya, Narutoshi
Yonezawa, Yasushige
Nakamura, Haruki
Fukuda, Ikuo
citation_publisher
AIP Publishing
citation_language
英語
citation_date
2012
citation_journal_title
The Journal of Chemical Physics
citation_volume
137
citation_firstpage
054314
citation_issn
00219606
10897690
citation_public_url
http://hdl.handle.net/11094/52401