Martínez L, Andrade R, Birgin E G, Martínez J M
Department of Physical Chemistry, IQ-UNICAMP, University of Campinas, Brazil.
J Comput Chem. 2009 Oct;30(13):2157-64. doi: 10.1002/jcc.21224.
Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from http://www.ime.unicamp.br/~martinez/packmol/.
分子动力学模拟的适当初始构型由分子在空间中的排列组成，其分布方式应能大致代表系统的整体结构。为了使模拟不会因大的范德华排斥相互作用而中断，不同分子的原子必须保持安全的成对距离。获得这样的分子排列可被视为一个堆积问题：每种类型的分子必须满足与系统几何形状相关的空间约束，并且不同分子的原子之间的距离必须大于某个指定的容差。我们已经开发了一种代码，能够将数百万个原子（这些原子组合成任意复杂的分子）堆积在各种三维区域内。这些区域可以是球体、椭圆体、圆柱体、平面或盒子的交集。用户只需提供每种类型的一个分子的结构以及每种类型的分子必须满足的几何约束。构建复杂的混合物、界面、在水中、其他溶剂或溶剂混合物中使生物分子溶剂化都很简单。此外，属于同一分子的不同原子也可以被限制在不同的空间区域，从而可以构建更有序的分子排列，如胶束、脂质双层等。在个人计算机中，最先进的分子动力学系统的堆积时间从几秒到几分钟不等。输入文件很简单，目前与PDB、Tinker、Molden或Moldy坐标文件兼容。该软件包作为免费软件分发，可从http://www.ime.unicamp.br/~martinez/packmol/下载。
