PACKMOL-GUI: An All-In-One VMD Interface for Efficient Molecular Packing

• DOI: 10.1021/acs.jcim.4c01639
• Publication Date: 2025-01-11T14:24:22Z
• Authors: Jian Huang; Chenchen Wu; Xiner Yang; Zaixing Yang; Shengtang Liu; Gang Yu
• Keywords: Chemical Physics (physics.chem-ph); Physics - Chemical Physics; FOS: Physical sciences

PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its perceivable advantages have been impeded by the long-standing 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 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 VMD and PACKMOL provides an intuitive and efficient all-in-one platform for the packing of complex molecular systems.