Constructing a Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with Periodic Boundary Conditions

机译：构造具有周期边界条件的分子动力学模拟的最小体积计算盒

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In many M.D. simulations the simulated system consists of a single macromolecule in a solvent. Usually, one is not interested in the behaviour of the solvent, so, the CPU time may be minimized by minimizing the amount of solvent. For a given molecule and cut-off radius this may be done by constructing a computational box with near minimal volume. In this article a method is presented to construct such a box, and the method is tested on a significant number of macromolecules. The volume of the resulting boxes proves to be typically 40% of the volume of usual boxes, and as a result the simulation time decreases with typically 60%.

机译：在许多医学博士模拟中，模拟系统由溶剂中的单个大分子组成。通常，人们对溶剂的行为不感兴趣，因此，可以通过减少溶剂量来最大程度地减少CPU时间。对于给定的分子和截止半径，这可以通过构建具有几乎最小体积的计算盒来完成。在本文中，提出了一种构建这种盒子的方法，并在大量的大分子上对该方法进行了测试。事实证明，生成的盒子的体积通常是普通盒子的40％，因此，仿真时间通常减少60％。

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《International Conference on Computational Science - ICCS 2003 Pt.3 Jun 2-4, 2003 Melbourne, Australia and St. Petersburg, Russia》|2003年|p.70-79|共10页
会议地点 Melbourne(AU) St. Petersburg(RU);Melbourne(AU) St. Petersburg(RU)
作者
Henk Bekker; Jur P. van den Berg; Tsjerk A. Wassenaar;
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Institute for Mathematics and Computing Science, University of Groningen, P.O.B. 800 9700 AV Groningen, The Netherlands;

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原文格式 PDF
正文语种 eng
中图分类自动化技术、计算机技术;
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专利

1. A Method to Obtain a Near-Minimal-Volume Molecular Simulation of a Macromolecule,Using Periodic Boundary Conditions and Rotational Constraints [J] . Henk Bekker, Jur P.LVan Den Berg, Tsjerk A.Wassenaar Journal of Computational Chemistry: Organic, Inorganic, Physical, Biological . 2004,第8期

机译：利用周期边界条件和旋转约束获取大分子近最小体积分子模拟的方法
2. Bacteriorhodopsin in a periodic boundary water-vacuum-water box as an example towards stable molecular dynamics simulations of G-protein coupled receptors. [J] . ter Laak-AM, Kuhne R Receptors and channels . 1999,第4期

机译：细菌视紫红质在周期性边界的水-真空-水箱中作为G蛋白偶联受体稳定分子动力学模拟的一个例子。
3. periodic-shell boundary condition for soft molecular systems: molecular dynamics simulations of flow past a circular cylinder [J] . Akira Satoh Molecular physics . 1997,第4期

机译：软分子系统的周期壳边界条件：绕圆柱体流动的分子动力学模拟
4. Constructing a Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with Periodic Boundary Conditions [C] . Henk Bekker, Jur P. van den Berg, Tsjerk A. Wassenaar International conference on computational science . 2003

机译：构建具有周期边界条件的分子动力学模拟的近极小卷计算盒
5. Molecular dynamics and continuum simulations of fluid flows with slip boundary conditions. [D] . Niavaranikheiri, Anoosheh. 2011

机译：具有滑移边界条件的流体流动的分子动力学和连续模拟。
6. Toward Improving Fidelity of Computational Fluid Dynamics Simulations: Boundary Conditions Matter [O] . Christof Karmonik 2014

机译：旨在提高计算流体动力学的保真性模拟：边界条件
7. Constructing a Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with Periodic Boundary Conditions [O] . Henk Bekker, Jur P. van den Berg, Tsjerk A. Wassenaar 2003

机译：构建具有周期边界条件的分子动力学模拟的近极小卷计算盒
8. Shock-Induced Shear Bands in an Energetic Molecular Crystal: Application of Shock-Front Absorbing Boundary Conditions to Molecular Dynamics Simulations [R] . Cawkwell, M. J., Sewell, T. D., Zheng, L., 2008

机译：高能分子晶体中的激波诱导剪切带：冲击前吸收边界条件在分子动力学模拟中的应用

Constructing a Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with Periodic Boundary Conditions

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