Ikeguchi Mitsunori
Graduate School of Integrated Science, Yokohama City University, 1-7-29, Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan.
J Comput Chem. 2004 Mar;25(4):529-41. doi: 10.1002/jcc.10402.
A partial rigid-body method of molecular dynamics simulations for proteins and membranes is presented. In this method, the symplectic integrator for rigid bodies is combined with the equations of motion for the NPT ensemble. The standard NPT ensemble is extended to the membrane-specific ensembles, the NPAT (constant normal pressure and lateral surface area of membranes and constant temperature) and NPgammaT (constant normal pressure and lateral surface tension of membranes and constant temperature) ensembles. By more than 30-ns simulations of aqueous proteins and hydrated lipid bilayers, the results of the partial rigid-body method demonstrated excellent conservation of total energy and consistent behavior with the traditional constraint method in terms of structural distribution and fluctuation of proteins and lipids. The efficient implementation of the partial rigid-body method in parallel computation is presented, which is shown to work well in large-scale molecular dynamics simulations.
本文提出了一种用于蛋白质和膜的分子动力学模拟的部分刚体方法。在该方法中，刚体的辛积分器与NPT系综的运动方程相结合。标准的NPT系综被扩展到特定于膜的系综，即NPAT（恒定法向压力、膜的横向表面积和恒定温度）和NPgammaT（恒定法向压力、膜的横向表面张力和恒定温度）系综。通过对水性蛋白质和水合脂质双层进行超过30纳秒的模拟，部分刚体方法的结果表明总能得到了很好的守恒，并且在蛋白质和脂质的结构分布和波动方面与传统约束方法具有一致的行为。本文还介绍了部分刚体方法在并行计算中的高效实现，结果表明该方法在大规模分子动力学模拟中运行良好。
