Bekker Henk, van den Berg Jur P, Wassenaar Tsjerk A
Institute for Mathematics and Computing Science, University of Groningen, P.O.B. 800 9700 AV Groningen, The Netherlands.
J Comput Chem. 2004 Jun;25(8):1037-46. doi: 10.1002/jcc.20050.
If the rotational motion of a single macromolecule is constrained during a molecular dynamics simulation with periodic boundary conditions it is possible to perform such simulations in a computational box with a minimal amount of solvent. In this article we describe a method to construct such a box, and test the approach on a number of macromolecules, randomly chosen from the protein databank. The essence of the method is that the molecule is first dilated with a layer of at least half the cut-off radius. For the enlarged molecule a near-densest lattice packing is calculated. From this packing the simulation box is derived. On average, the volume of the resulting box proves to be about 50% of the volume of standard boxes. In test simulations this yields on average a factor of about two in simulation speed.
如果在具有周期性边界条件的分子动力学模拟过程中，单个大分子的旋转运动受到限制，那么就有可能在含有最少量溶剂的计算盒中进行此类模拟。在本文中，我们描述了一种构建这种盒子的方法，并在从蛋白质数据库中随机选取的多个大分子上测试了该方法。该方法的核心是，首先用一层至少为截止半径一半的溶剂层来扩张分子。对于扩张后的分子，计算其近乎最密集的晶格堆积。由此堆积推导出模拟盒。平均而言，所得盒子的体积约为标准盒子体积的50%。在测试模拟中，这平均使模拟速度提高约两倍。
