Yang Darian T, Chong Lillian T
bioRxiv. 2024 May 21:2024.05.18.594829. doi: 10.1101/2024.05.18.594829.
Given the growing interest in path sampling methods for extending the timescales of molecular dynamics (MD) simulations, there has been great interest in software tools that streamline the generation of plots for monitoring the progress of large-scale simulations. Here, we present the WEDAP Python package for simplifying the analysis of data generated from either conventional MD simulations or the weighted ensemble (WE) path sampling method, as implemented in the widely used WESTPA software package. WEDAP facilitates (i) the parsing of WE simulation data stored in highly compressed, hierarchical HDF5 files, and (ii) incorporates trajectory weights from WE simulations into all generated plots. Our Python package consists of multiple user-friendly interfaces: a command-line interface, a graphical user interface, and a Python application programming interface. We demonstrate the plotting features of WEDAP through a series of examples using data from WE and conventional MD simulations that focus on the HIV-1 capsid protein C-terminal domain dimer as a showcase system. The source code for WEDAP is freely available on GitHub at https://github.com/chonglab-pitt/wedap .
鉴于人们对用于扩展分子动力学（MD）模拟时间尺度的路径采样方法的兴趣日益浓厚，因此对能够简化大规模模拟进程监测图生成的软件工具也产生了极大兴趣。在此，我们展示了WEDAP Python软件包，用于简化对常规MD模拟或加权系综（WE）路径采样方法生成的数据的分析，该方法在广泛使用的WESTPA软件包中实现。WEDAP有助于（i）解析存储在高度压缩的分层HDF5文件中的WE模拟数据，以及（ii）将WE模拟的轨迹权重纳入所有生成的图中。我们的Python软件包由多个用户友好的接口组成：命令行接口、图形用户界面和Python应用程序编程接口。我们通过一系列示例展示了WEDAP的绘图功能，这些示例使用了来自WE和常规MD模拟的数据，重点是将HIV-1衣壳蛋白C末端结构域二聚体作为一个展示系统。WEDAP的源代码可在GitHub上免费获取，网址为https://github.com/chonglab-pitt/wedap 。
