de Souza O N, Ornstein R L
Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
Biophys J. 1997 Jun;72(6):2395-7. doi: 10.1016/S0006-3495(97)78884-2.
The particle-mesh Ewald (PME) method is considered to be both efficient and accurate for the evaluation of long-range electrostatic interactions in large macromolecular systems being studied by molecular dynamics simulations. This method assumes "infinite" periodic boundary conditions resembling the symmetry of a crystal environment. Can such a "solid-state" method accurately portray a macromolecular solute such as DNA in solution? To address this issue, we have performed three 1500-ps PME molecular dynamics (MD) simulations, each with a different box size, on the d(CGCGA6CG)-(CGT6CGCG) DNA dodecamer. The smallest box had the DNA solvated by a layer of water molecules of at least 5 A along each orthogonal direction. The intermediate size box and the largest box had the DNA solvated by a layer of water molecules of at least 10 A and 15 A, respectively, along each orthogonal direction. The intermediate size box in the present study is similar to the box size currently chosen by most workers in the field. Based on a comparison of RMSDs and curvature for this single DNA dodecamer sequence, the larger two box sizes do not appear to afford any extra benefit over the smallest box. The implications of this finding are briefly discussed.
粒子网格埃瓦尔德（PME）方法被认为在通过分子动力学模拟研究的大型大分子系统中评估长程静电相互作用时既高效又准确。该方法假设“无限”周期性边界条件，类似于晶体环境的对称性。这样一种“固态”方法能否准确描绘溶液中的大分子溶质，如DNA呢？为了解决这个问题，我们对d（CGCGA6CG）-（CGT6CGCG）十二聚体DNA进行了三次1500皮秒的PME分子动力学（MD）模拟，每次模拟的盒子大小不同。最小的盒子中，DNA被沿每个正交方向至少5埃厚的一层水分子溶剂化。中等大小的盒子和最大的盒子中，DNA分别被沿每个正交方向至少10埃和15埃厚的一层水分子溶剂化。本研究中的中等大小盒子与该领域目前大多数研究人员所选择的盒子大小相似。基于对该单一DNA十二聚体序列的均方根偏差（RMSDs）和曲率的比较，较大的两种盒子大小似乎并没有比最小的盒子带来任何额外的优势。我们简要讨论了这一发现的意义。
