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A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics.
Kazuaki Z Takahashi1, Tetsu Narumi, Kenji Yasuoka
1Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan. saepon@a3.keio.jp
The Journal of Chemical Physics
|November 11, 2011
Summary
The new IPSp/Tree method accurately simulates large molecular systems, showing minimal error in Coulombic force calculations for bulk water. This efficient technique is suitable for predicting water
Area of Science:
- Computational Chemistry
- Molecular Dynamics
- Physical Chemistry
Background:
- Large-scale molecular dynamics simulations require efficient methods for calculating long-range interactions.
- Existing methods like IPS/DFFT offer efficiency but their accuracy in combination with tree-based structures needs evaluation.
- The isotropic periodic sum (IPS) method has two versions, IPSn for point charges and IPSp for polar molecules.
Purpose of the Study:
- To evaluate the accuracy of the combined IPS/Tree method for large-scale molecular dynamics simulations.
- To assess the performance of IPSn/Tree and IPSp/Tree in calculating Coulombic forces and physical properties of bulk water.
- To determine if the tree-based algorithm can be successfully integrated with the IPSp method.
Main Methods:
- Development of the IPS/Tree method, combining isotropic periodic sum (IPS) and tree-based approaches.
- Application of IPSn/Tree and IPSp/Tree to molecular dynamics simulations of 32,000 bulk water molecules.
- Evaluation of Coulombic force accuracy, self-diffusion, and radial distribution functions against the Ewald method.
Main Results:
- The IPSp/Tree method demonstrated reasonably small errors in Coulombic force calculations, comparable to the theoretical error of standard tree-based methods.
- The IPSn/Tree method exhibited a relatively large error, potentially due to the original IPSn method's interaction treatment.
- Both IPSn/Tree and IPSp/Tree showed good agreement with the Ewald method for self-diffusion and radial distribution functions of water.
Conclusions:
- The IPSp/Tree method is a viable and accurate technique for large-scale simulations of polar molecules.
- The tree-based algorithm is successfully integrated with the IPSp method for efficient and accurate simulations.
- IPSp/Tree offers a potentially fast and accurate approach for predicting transport coefficients and liquid structures in homogeneous systems.
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