Literature DB >> 22894355

Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water.

Ikuo Fukuda1, Narutoshi Kamiya, Yasushige Yonezawa, Haruki Nakamura.   

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)], 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.

Entities:  

Mesh:

Substances:

Year:  2012        PMID: 22894355     DOI: 10.1063/1.4739789

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


  13 in total

Review 1.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

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

Authors:  Junichi Higo; Kota Kasahara; Mitsuhito Wada; Bhaskar Dasgupta; Narutoshi Kamiya; Tomonori Hayami; Ikuo Fukuda; Yoshifumi Fukunishi; Haruki Nakamura
Journal:  Protein Eng Des Sel       Date:  2019-12-31       Impact factor: 1.650

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

Authors:  Tomomi Ukawa; Fumihiko Banno; Toshiki Ishikawa; Kota Kasahara; Yuuta Nishina; Rika Inoue; Keigo Tsujii; Masatoshi Yamaguchi; Takuya Takahashi; Yoichiro Fukao; Maki Kawai-Yamada; Minoru Nagano
Journal:  Plant Physiol       Date:  2022-06-01       Impact factor: 8.005

4.  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

5.  Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.

Authors:  Takamasa Arakawa; Narutoshi Kamiya; Haruki Nakamura; Ikuo Fukuda
Journal:  PLoS One       Date:  2013-10-04       Impact factor: 3.240

6.  A novel approach of dynamic cross correlation analysis on molecular dynamics simulations and its application to Ets1 dimer-DNA complex.

Authors:  Kota Kasahara; Ikuo Fukuda; Haruki Nakamura
Journal:  PLoS One       Date:  2014-11-07       Impact factor: 3.240

7.  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

8.  Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling.

Authors:  Shinji Iida; Tadaaki Mashimo; Takashi Kurosawa; Hironobu Hojo; Hiroya Muta; Yuji Goto; Yoshifumi Fukunishi; Haruki Nakamura; Junichi Higo
Journal:  J Comput Chem       Date:  2016-10-13       Impact factor: 3.376

9.  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

10.  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

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.