Yoneda S
School of Science, Kitasato University, Kanagawa-Ken, Japan.
J Mol Graph Model. 1997 Aug;15(4):233-7, 260. doi: 10.1016/s1093-3263(97)00081-8.
One of the most accurate styles of protein simulation is to calculate proteins in crystalline environment without neglect of long-range interactions. The long-range interactions can be accelerated by various methods. However, as a unit cell of a protein crystal is a large molecular assembly, its simulation is still unpractical without high-speed computers. Thus this article is addressed to the reduction of calculational volumes for protein crystal simulation by a further implementation of the rotational symmetry boundary condition method. For protein crystals in P4(3)2(1)2 symmetry, a computational cell and related tables were developed. A 120-ps molecular dynamics simulation was performed for a P4(3)2(1)2 symmetry crystal of glycogen phosphorylase b under rotational symmetry boundary conditions. The computational cell was one-eighth of the unit cell in volume, and less than about one-fourth of the conventional periodic boundary box. Generation of neighbor atom pair lists was greatly accelerated, and thus the simulation was practical even with a personal computer.
最精确的蛋白质模拟方式之一是在不忽略长程相互作用的情况下，在晶体环境中计算蛋白质。长程相互作用可以通过各种方法加速。然而，由于蛋白质晶体的一个晶胞是一个大分子聚集体，没有高速计算机的话，其模拟仍然不切实际。因此，本文旨在通过进一步实施旋转对称边界条件方法来减少蛋白质晶体模拟的计算量。对于具有P4(3)2(1)2对称性的蛋白质晶体，开发了一个计算单元和相关表格。在旋转对称边界条件下，对糖原磷酸化酶b的P4(（3）2(1)2对称性晶体进行了120皮秒的分子动力学模拟。该计算单元的体积是晶胞的八分之一，小于传统周期性边界框的约四分之一。相邻原子对列表的生成大大加速，因此即使使用个人计算机，模拟也切实可行。
