### Abstract

An IPS/Tree method which is a combination of the isotropic periodic sum (IPS) method and tree-based method was developed for large-scale molecular dynamics simulations, such as biological and polymer systems, that need hundreds of thousands of molecules. The tree-based method uses a hierarchical tree structure to reduce the calculation cost of long-range interactions. IPS/Tree is an efficient method like IPS/DFFT, which is a combination of the IPS method and FFT in calculating large-scale systems that require massively parallel computers. The IPS method has two different versions: IPSn and IPSp. The basic idea is the same expect for the fact that the IPSn method is applied to calculations for point charges, while the IPSp method is used to calculate polar molecules. The concept of the IPS/Tree method is available for both IPSn and IPSp as IPSn/Tree and IPSp/Tree. Even though the accuracy of the Coulomb forces with tree-based method is well known, the accuracy for the combination of the IPS and tree-based methods is unclear. Therefore, in order to evaluate the accuracy of the IPS/Tree method, we performed molecular dynamics simulations for 32 000 bulk water molecules, which contains around 10^{5} point charges. IPSn/Tree and IPSp/Tree were both applied to study the interaction calculations of Coulombic forces. The accuracy of the Coulombic forces and other physical properties of bulk water systems were evaluated. The IPSp/Tree method not only has reasonably small error in estimating Coulombic forces but the error was almost the same as the theoretical error of the ordinary tree-based method. These facts show that the algorithm of the tree-based method can be successfully applied to the IPSp method. On the other hand, the IPSn/Tree has a relatively large error, which seems to have been derived from the interaction treatment of the original IPSn method. The self-diffusion and radial distribution functions of water were calculated each by both the IPSn/Tree and IPSp/Tree methods, where both methods showed reasonable agreement with the Ewald method. In conclusion, the IPSp/Tree method is a potentially fast and sufficiently accurate technique for predicting transport coefficients and liquid structures of water in a homogeneous system.

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

Article number | 174108 |

Journal | Journal of Chemical Physics |

Volume | 135 |

Issue number | 17 |

DOIs | |

Publication status | Published - 2011 Nov 7 |

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### ASJC Scopus subject areas

- Physics and Astronomy(all)
- Physical and Theoretical Chemistry

### Cite this

*Journal of Chemical Physics*,

*135*(17), [174108]. https://doi.org/10.1063/1.3658640

**A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics.** / Takahashi, Kazuaki Z.; Narumi, Tetsu; Yasuoka, Kenji.

Research output: Contribution to journal › Article

*Journal of Chemical Physics*, vol. 135, no. 17, 174108. https://doi.org/10.1063/1.3658640

}

TY - JOUR

T1 - A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics

AU - Takahashi, Kazuaki Z.

AU - Narumi, Tetsu

AU - Yasuoka, Kenji

PY - 2011/11/7

Y1 - 2011/11/7

N2 - An IPS/Tree method which is a combination of the isotropic periodic sum (IPS) method and tree-based method was developed for large-scale molecular dynamics simulations, such as biological and polymer systems, that need hundreds of thousands of molecules. The tree-based method uses a hierarchical tree structure to reduce the calculation cost of long-range interactions. IPS/Tree is an efficient method like IPS/DFFT, which is a combination of the IPS method and FFT in calculating large-scale systems that require massively parallel computers. The IPS method has two different versions: IPSn and IPSp. The basic idea is the same expect for the fact that the IPSn method is applied to calculations for point charges, while the IPSp method is used to calculate polar molecules. The concept of the IPS/Tree method is available for both IPSn and IPSp as IPSn/Tree and IPSp/Tree. Even though the accuracy of the Coulomb forces with tree-based method is well known, the accuracy for the combination of the IPS and tree-based methods is unclear. Therefore, in order to evaluate the accuracy of the IPS/Tree method, we performed molecular dynamics simulations for 32 000 bulk water molecules, which contains around 105 point charges. IPSn/Tree and IPSp/Tree were both applied to study the interaction calculations of Coulombic forces. The accuracy of the Coulombic forces and other physical properties of bulk water systems were evaluated. The IPSp/Tree method not only has reasonably small error in estimating Coulombic forces but the error was almost the same as the theoretical error of the ordinary tree-based method. These facts show that the algorithm of the tree-based method can be successfully applied to the IPSp method. On the other hand, the IPSn/Tree has a relatively large error, which seems to have been derived from the interaction treatment of the original IPSn method. The self-diffusion and radial distribution functions of water were calculated each by both the IPSn/Tree and IPSp/Tree methods, where both methods showed reasonable agreement with the Ewald method. In conclusion, the IPSp/Tree method is a potentially fast and sufficiently accurate technique for predicting transport coefficients and liquid structures of water in a homogeneous system.

AB - An IPS/Tree method which is a combination of the isotropic periodic sum (IPS) method and tree-based method was developed for large-scale molecular dynamics simulations, such as biological and polymer systems, that need hundreds of thousands of molecules. The tree-based method uses a hierarchical tree structure to reduce the calculation cost of long-range interactions. IPS/Tree is an efficient method like IPS/DFFT, which is a combination of the IPS method and FFT in calculating large-scale systems that require massively parallel computers. The IPS method has two different versions: IPSn and IPSp. The basic idea is the same expect for the fact that the IPSn method is applied to calculations for point charges, while the IPSp method is used to calculate polar molecules. The concept of the IPS/Tree method is available for both IPSn and IPSp as IPSn/Tree and IPSp/Tree. Even though the accuracy of the Coulomb forces with tree-based method is well known, the accuracy for the combination of the IPS and tree-based methods is unclear. Therefore, in order to evaluate the accuracy of the IPS/Tree method, we performed molecular dynamics simulations for 32 000 bulk water molecules, which contains around 105 point charges. IPSn/Tree and IPSp/Tree were both applied to study the interaction calculations of Coulombic forces. The accuracy of the Coulombic forces and other physical properties of bulk water systems were evaluated. The IPSp/Tree method not only has reasonably small error in estimating Coulombic forces but the error was almost the same as the theoretical error of the ordinary tree-based method. These facts show that the algorithm of the tree-based method can be successfully applied to the IPSp method. On the other hand, the IPSn/Tree has a relatively large error, which seems to have been derived from the interaction treatment of the original IPSn method. The self-diffusion and radial distribution functions of water were calculated each by both the IPSn/Tree and IPSp/Tree methods, where both methods showed reasonable agreement with the Ewald method. In conclusion, the IPSp/Tree method is a potentially fast and sufficiently accurate technique for predicting transport coefficients and liquid structures of water in a homogeneous system.

UR - http://www.scopus.com/inward/record.url?scp=80855156845&partnerID=8YFLogxK

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U2 - 10.1063/1.3658640

DO - 10.1063/1.3658640

M3 - Article

C2 - 22070293

AN - SCOPUS:80855156845

VL - 135

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

SN - 0021-9606

IS - 17

M1 - 174108

ER -