### Abstract

Molecular dynamics simulation has been applied for water to compare the isotropic periodic sum (IPS) method for polar molecules (IPSp) to the normal IPS (IPSn) method and the Ewald sum by evaluating the diffusion coefficient and liquid structure. In our previous study, we have applied the IPSn method for bulk water and found notable deviation of the radial distribution function g(r). In this work, the IPSp gives a good estimation for the potential energy and the self-diffusion coefficient at a cut-off radius, r _{c}, greater than 2.2nm while avoiding the notable deviation of g(r) which appeared in the case of IPSn. The distance-dependent Kirkwood factor G _{k}(r) was also calculated, and the truncation of a long-range interaction of the cut-off-like method (such as cut-off with or without the switch function and the reaction field) shows serious shortcomings for dipole-dipole correlations in bulk water systems. This was observed by comparing the shape to that of the Ewald sum. G _{k}(r) of the cut-off-like method greatly deviates from that of the Ewald sum. However, the discrepancy of G _{k}(r) for IPSp method was found to be much less than that of other typical cut-off-like methods. We conclude that the IPSp method is an adequately accurate technique for estimating transport coefficients and the liquid structure of water in a homogeneous system at long cut-off distances.

Original language | English |
---|---|

Pages (from-to) | 397-403 |

Number of pages | 7 |

Journal | Molecular Simulation |

Volume | 38 |

Issue number | 5 |

DOIs | |

Publication status | Published - 2012 Apr 1 |

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### Keywords

- cut-off method
- long-range interaction
- molecular dynamics simulation

### ASJC Scopus subject areas

- Condensed Matter Physics
- Modelling and Simulation
- Chemistry(all)
- Chemical Engineering(all)
- Materials Science(all)
- Information Systems

### Cite this

*Molecular Simulation*,

*38*(5), 397-403. https://doi.org/10.1080/08927022.2010.547857

**Cut-off radius effect of the isotropic periodic sum method for polar molecules in a bulk water system.** / Takahashi, Kazuaki; Narumi, Tetsu; Yasuoka, Kenji.

Research output: Contribution to journal › Article

*Molecular Simulation*, vol. 38, no. 5, pp. 397-403. https://doi.org/10.1080/08927022.2010.547857

}

TY - JOUR

T1 - Cut-off radius effect of the isotropic periodic sum method for polar molecules in a bulk water system

AU - Takahashi, Kazuaki

AU - Narumi, Tetsu

AU - Yasuoka, Kenji

PY - 2012/4/1

Y1 - 2012/4/1

N2 - Molecular dynamics simulation has been applied for water to compare the isotropic periodic sum (IPS) method for polar molecules (IPSp) to the normal IPS (IPSn) method and the Ewald sum by evaluating the diffusion coefficient and liquid structure. In our previous study, we have applied the IPSn method for bulk water and found notable deviation of the radial distribution function g(r). In this work, the IPSp gives a good estimation for the potential energy and the self-diffusion coefficient at a cut-off radius, r c, greater than 2.2nm while avoiding the notable deviation of g(r) which appeared in the case of IPSn. The distance-dependent Kirkwood factor G k(r) was also calculated, and the truncation of a long-range interaction of the cut-off-like method (such as cut-off with or without the switch function and the reaction field) shows serious shortcomings for dipole-dipole correlations in bulk water systems. This was observed by comparing the shape to that of the Ewald sum. G k(r) of the cut-off-like method greatly deviates from that of the Ewald sum. However, the discrepancy of G k(r) for IPSp method was found to be much less than that of other typical cut-off-like methods. We conclude that the IPSp method is an adequately accurate technique for estimating transport coefficients and the liquid structure of water in a homogeneous system at long cut-off distances.

AB - Molecular dynamics simulation has been applied for water to compare the isotropic periodic sum (IPS) method for polar molecules (IPSp) to the normal IPS (IPSn) method and the Ewald sum by evaluating the diffusion coefficient and liquid structure. In our previous study, we have applied the IPSn method for bulk water and found notable deviation of the radial distribution function g(r). In this work, the IPSp gives a good estimation for the potential energy and the self-diffusion coefficient at a cut-off radius, r c, greater than 2.2nm while avoiding the notable deviation of g(r) which appeared in the case of IPSn. The distance-dependent Kirkwood factor G k(r) was also calculated, and the truncation of a long-range interaction of the cut-off-like method (such as cut-off with or without the switch function and the reaction field) shows serious shortcomings for dipole-dipole correlations in bulk water systems. This was observed by comparing the shape to that of the Ewald sum. G k(r) of the cut-off-like method greatly deviates from that of the Ewald sum. However, the discrepancy of G k(r) for IPSp method was found to be much less than that of other typical cut-off-like methods. We conclude that the IPSp method is an adequately accurate technique for estimating transport coefficients and the liquid structure of water in a homogeneous system at long cut-off distances.

KW - cut-off method

KW - long-range interaction

KW - molecular dynamics simulation

UR - http://www.scopus.com/inward/record.url?scp=80855159115&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80855159115&partnerID=8YFLogxK

U2 - 10.1080/08927022.2010.547857

DO - 10.1080/08927022.2010.547857

M3 - Article

AN - SCOPUS:80855159115

VL - 38

SP - 397

EP - 403

JO - Molecular Simulation

JF - Molecular Simulation

SN - 0892-7022

IS - 5

ER -