Fast algorithms for accurate molecular dynamics simulations of membrane proteins

用于膜蛋白精确分子动力学模拟的快速算法

• 批准号: 16500187
• 负责人: AMISAKI Takashi
• 金额: $ 2.24万
• 依托单位: National University Corporation Tottori University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2004
• 资助国家: 日本
• 起止时间: 2004 至 2005
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-16500187/
• 关键词: molecular dynamics calculation; membrane proteins; periodic boundary conditions; fast multipole method; 擬二次元周期性; 薬物動態学

To compress the costs of the molecular dynamics simulations of biomolecules, Coulomb interactions are usually calculated using fast algorithms, such as the fast multipole method (FMM) and particle mesh Ewald (PME). On the other hand, in biomembrane simulations, it is usual to repeat membranes in the z-axis direction so as to constitute a three-dimensional periodicity, which can then be directly handled by PME and periodic FMM. However, the artificial repeat of the membrane may cause undesirable artifacts on the simulations. In this work, we originally aimed at developing a periodic FMM that will circumvent such artifacts. We first derived the formula for virials in the framework of the FMM theory, which are necessary for constant-pressure simulation. We found that the conversion of the multipole to local expansion, which is the key operation of FMM, affects the virials in two ways : through lattice-dependence of the conversion matrix and through that of the multipoles. The latter contribution has not been reported previously. The FMM computation is then O(NlogN) instead of O(N). The results of numerical tests also suggest that the net dipole of the unit cell produces a serious effect on the precision of the Coulomb interactions and hence it is equally important to develop an effective strategy for removing the effect, although the development is left for future work. On the other hand, periodic FMMs generally suffer from great deal of computation regarding interaction between neighboring cells. In this work, a cluster computing system, which is based on the cooperation of FMM algorithm and dedicated hardware for the Coulomb-force evaluation, was developed and improved. Currently, further investigation on the accurate virial calculation is being undertaken, which is necessary for producing accurate FMM calculation as well as for reducing artifacts that may be caused by the periodicity.

为了压缩生物分子的分子动力学模拟的成本，通常使用快速算法（例如快速多极方法（FMM）和粒子网眼Ewald（PME）计算库仑相互作用。另一方面，在生物膜模拟中，通常在Z轴方向上重复膜以构成三维周期性，然后可以通过PME和周期性FMM直接处理。但是，膜的人工重复可能会在模拟上引起不良的伪影。在这项工作中，我们最初旨在开发一种定期的FMM，以规避此类文物。我们首先在FMM理论的框架中得出了病毒级的公式，这对于恒压模拟是必不可少的。我们发现，多极向局部膨胀的转化是FMM的关键操作，它以两种方式影响病毒：通过转换矩阵的晶格依赖性以及通过多物的晶格依赖性。后者的贡献先前尚未报道。然后，FMM计算为O（nlogn），而不是O（n）。数值测试的结果还表明，单位电池的净偶极子对库仑相互作用的精度产生了严重的影响，因此制定有效的消除效果的有效策略同样重要，尽管该开发是将来的发展。另一方面，周期性的FMM通常会遭受有关相邻细胞之间相互作用的大量计算。在这项工作中，开发和改进了基于FMM算法和专用硬件的集群计算系统，该系统的合作是开发和改进的。当前，正在进行对准确的病毒计算的进一步研究，这对于产生准确的FMM计算以及减少可能由周期性引起的伪像所必需。