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学術雑誌論文

学術雑誌論文

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The Journal of Chemical Physics.137 P.054314

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

AIP Publishing

英語

2012

http://hdl.handle.net/11094/52401

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

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.

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.

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

AIP Publishing

英語

2012

The Journal of Chemical Physics

137

054314

http://hdl.handle.net/11094/52401