Partial rigid-body dynamics in NPT, NPAT and NPγT ensembles for proteins and membranes
Partial rigid-body dynamics in NPT, NPAT and NPγT ensembles for proteins and membranes
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DOI：
10.1002/jcc.10402
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发表时间：
2004-03-01
影响因子：
3
通讯作者：
Ikeguchi, M
中科院分区：
文献类型：
--
作者：
Ikeguchi, M
提出了蛋白质和膜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 NPT 系综扩展到膜特定系综、NPAT（膜的恒定法向压力和侧表面面积以及恒温）和 NPgammaT（膜的恒定法向压力和侧表面张力以及恒温）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显示出优异的总能量守恒性，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表现一致。提出了并行计算中部分刚体方法的有效实现，该方法在大规模分子动力学模拟中表现良好。 (C) 2004 年 Wiley 期刊公司。
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. (C) 2004 Wiley Periodicals, Inc.