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atom: A MATLAB PACKAGE FOR MANIPULATION OF MOLECULAR SYSTEMS
Clays and Clay Minerals ( IF 2.2 ) Pub Date : 2019-10-01 , DOI: 10.1007/s42860-019-00043-y
Michael Holmboe

This work presents Atomistic Topology Operations in MATLAB (atom), an open source library of modular MATLAB routines which comprise a general and flexible framework for manipulation of atomistic systems. The purpose of the atom library is simply to facilitate common operations performed for construction, manipulation, or structural analysis. Due to the data structure used, atoms and molecules can be operated upon based on different chemical names or attributes, such as atom- or molecule-ID, name, residue name, charge, positions, etc. Furthermore, the Bond Valence Method and a neighbor-distance analysis can be performed to assign many chemical properties of inorganic molecules. Apart from reading and writing common coordinate files (.pdb, .xyz, .gro, .cif) and trajectories (.dcd, .trr, .xtc; binary formats are parsed via third-party packages), the atom library can also be used to generate topology files with bonding and angle information taking the periodic boundary conditions into account, and supports basic Gromacs, NAMD, LAMMPS, and RASPA2 topology file formats. Focusing on clay-mineral systems, the library supports CLAYFF (Cygan, 2004) but can also generate topology files for the INTERFACE forcefield (Heinz, 2005, 2013) for Gromacs and NAMD.

中文翻译:

atom:用于操纵分子系统的 MATLAB 包

这项工作介绍了 MATLAB (atom) 中的原子拓扑操作,这是一个模块化 MATLAB 例程的开源库,其中包含用于操作原子系统的通用且灵活的框架。原子库的目的只是促进为构造、操作或结构分析执行的常见操作。由于使用的数据结构,原子和分子可以基于不同的化学名称或属性进行操作,例如原子或分子 ID、名称、残基名称、电荷、位置等。 此外,键价方法和可以进行近邻距离分析来分配无机分子的许多化学性质。除了读写常见的坐标文件(.pdb、.xyz、.gro、.cif)和轨迹(.dcd、.trr、.xtc;二进制格式通过第三方包解析),原子库还可用于生成具有键合和角度信息的拓扑文件,并考虑到周期性边界条件,并支持基本的 Gromacs、NAMD、LAMMPS 和 RASPA2 拓扑文件格式。该库专注于粘土矿物系统,支持 CLAYFF(Cygan,2004),但也可以为 Gromacs 和 NAMD 的 INTERFACE 力场(Heinz,2005,2013)生成拓扑文件。
更新日期:2019-10-01
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