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Journal of Chemical Physics / Volume 135 / Issue 17 / ARTICLES / Theoretical Methods and Algorithms

J. Chem. Phys. 135, 174108 (2011); http://dx.doi.org/10.1063/1.3658640 (9 pages)

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

Kazuaki Z. Takahashi1, Tetsu Narumi2, and Kenji Yasuoka1

1Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
2Department of Computer Science, University of Electro-Communications, Tokyo 182-8585, Japan

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(Received 19 July 2011; accepted 17 October 2011; published online 2 November 2011)

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.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. METHODS
    1. Tree-based method
    2. IPS method
    3. IPS/Tree method
    4. MD simulations
  3. RESULTS AND DISCUSSION
    1. Accuracy of Coulombic forces
    2. Potential energy and self-diffusion
    3. Radial distribution function
  4. CONCLUSION

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KEYWORDS and PACS

Keywords

biodiffusion, liquid structure, long-range order, molecular biophysics, molecular dynamics method, self-diffusion, trees (mathematics), water

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3658640

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
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