Faculty of Physics, University of Vienna, Boltzmangasse 5, Vienna A-1090, Austria.
Institut UTINAM (CNRS UMR 6213), Université Bourgogne Franche-Comté, 16 Route de Gray, Besançon Cedex F-25030, France.
J Comput Chem. 2018 Sep 30;39(25):2118-2125. doi: 10.1002/jcc.25384. Epub 2018 Oct 10.
Pytim is a versatile python framework for the analysis of interfacial properties in molecular simulations. The code implements several algorithms for the identification of instantaneous interfaces of arbitrary shape, and analysis tools written specifically for the study of interfacial properties, such as intrinsic profiles. The code is written in the python language, and makes use of the numpy and scipy packages to deliver high computational performances. Pytim relies on the MDAnalysis library to analyze the trajectory file formats of popular simulation packages such as gromacs, charmm, namd, lammps or Amber, and can be used to steer OpenMM simulations. Pytim can write information about surfaces and surface atomic layers to vtk, cube, and pdb files for easy visualization. The classes of Pytim can be easily customized and extended to include new interfacial algorithms or analysis tools. The code is available as open source and is free of charge. © 2018 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
Pytim 是一个用于分析分子模拟中界面性质的多功能 Python 框架。该代码实现了几种用于识别任意形状瞬时界面的算法，以及专门用于研究界面性质的分析工具，如本征分布。该代码是用 Python 语言编写的，并利用 numpy 和 scipy 包来实现高计算性能。Pytim 依赖于 MDAnalysis 库来分析流行的模拟包（如 gromacs、charmm、namd、lammps 或 Amber）的轨迹文件格式，并可用于引导 OpenMM 模拟。Pytim 可以将有关表面和表面原子层的信息写入 vtk、cube 和 pdb 文件，以便于可视化。Pytim 的类可以轻松定制和扩展，以包括新的界面算法或分析工具。该代码是开源的，免费使用。© 2018 作者。Wiley Periodicals, Inc. 出版的《计算化学杂志》
