Atomistic Simulation Centre, School of Maths and Physics, Queen's University Belfast, Belfast, BT7 1NN, United Kingdom.
J Comput Chem. 2010 Feb;31(3):639-48. doi: 10.1002/jcc.21359.
Aten is a tool for Linux, Mac, and Windows platforms to ease the creation, editing, and visualization of coordinates for use in, for example, molecular dynamics simulations. The code handles gas-phase molecules in addition to crystals, surfaces, and liquids, providing standard tools to edit "by the atom" along with specific "by the box" methods suited to periodic systems, including full crystallographic spacegroup packing definitions. Visualization of systems encompasses the standard drawing styles and may be mixed with an arbitrary number of other basic objects, such as arrows and geometric objects allowing creation of scenes involving vector fields, coarse-grained particles, etc. Standard molecular mechanics forcefields can be read in, edited, applied to molecules using the built-in chemical typing language, and subsequently used to calculate energies and forces, minimize energies with respect to coordinates, decompose energies into contribution by molecule type, etc. Monte Carlo methods are available with which to generate random configurations of N-component systems, or solvate around molecules or in specific regions within existing configurations. Supported file formats are governed by user-defined "filters," which provide flexibility of input/output as well as the ability to define custom or extended formats of traditional files. Forcefield descriptions for loaded systems can be output and formatted for use as input to common codes. All features can be accessed by a comprehensive GUI and scripting language based on the C syntax.
Aten 是一个适用于 Linux、Mac 和 Windows 平台的工具，用于简化坐标的创建、编辑和可视化，例如在分子动力学模拟中使用。该代码除了处理气相分子外，还处理晶体、表面和液体，提供了用于“按原子”编辑的标准工具，以及适用于周期性系统的特定“按盒子”方法，包括完整的晶体学点群包装定义。系统的可视化包括标准的绘图样式，并可以与任意数量的其他基本对象（如箭头和几何对象）混合使用，从而可以创建涉及矢量场、粗粒粒子等的场景。可以读取标准的分子力学力场，进行编辑，使用内置的化学类型化语言应用于分子，然后用于计算能量和力，根据坐标最小化能量，将能量分解为分子类型的贡献等。提供了 Monte Carlo 方法，可用于生成 N 组分系统的随机配置，或在现有配置中的分子周围或特定区域中溶剂化。支持的文件格式由用户定义的“过滤器”控制，这些过滤器提供了输入/输出的灵活性，以及定义自定义或扩展传统文件格式的能力。加载系统的力场描述可以输出并格式化，用作常见代码的输入。所有功能都可以通过基于 C 语法的全面 GUI 和脚本语言访问。
