Huang Jian, Wu Chenchen, Yang Xiner, Yang Zaixing, Liu Shengtang, Yu Gang
Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province, Hangzhou 310052, China.
National Clinical Research Center for Child Health, National Children's Regional Medical Center, Zhejiang University School of Medicine , Children's Hospital, Hangzhou 310052, China.
J Chem Inf Model. 2025 Jan 27;65(2):778-784. doi: 10.1021/acs.jcim.4c01639. Epub 2025 Jan 11.
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its tremendous advantages have been impeded by the longstanding lack of a robust open-source graphical user interface (GUI) that integrates parameter settings with the visualization of molecular and geometric constraints. To address this limitation, we have developed PACKMOL-GUI, a VMD plugin that leverages the dynamic extensibility of the Tcl/Tk toolkit. This GUI enables the configuration of all PACKMOL parameters through an intuitive user panel, while also facilitating the visualization of molecular structures and geometric constraints, including cubes, boxes, and spheres, among others via the VMD software. The seamless interaction between the VMD and PACKMOL provides an intuitive and efficient all-in-one platform for the packing of complex molecular systems.
PACKMOL是计算化学领域广泛使用的分子建模工具。然而，由于长期缺乏一个强大的开源图形用户界面（GUI），其巨大优势受到了阻碍，该界面应将参数设置与分子和几何约束的可视化集成在一起。为了解决这一限制，我们开发了PACKMOL-GUI，这是一个VMD插件，它利用了Tcl/Tk工具包的动态可扩展性。这个GUI通过直观的用户面板实现了所有PACKMOL参数的配置，同时还通过VMD软件促进了分子结构和几何约束（包括立方体、盒子和球体等）的可视化。VMD和PACKMOL之间的无缝交互为复杂分子系统的堆积提供了一个直观且高效的一体化平台。
