Web-PackMol: A Molecular Packing Tool for the Web Browser

Adequate initial configurations for molecular dynamics (MD) simulations are essential for preventing unphysical overlaps that disrupt integration algorithms. Most software packages for MD simulation already bring a "solvation" function that handles that specific part of the setup, producing regular boxes for MD. But these programs cannot deal with more complex molecule packing procedures. While the original PACKMOL package introduced a powerful gradient-based optimization for this purpose, its command-line nature and installation requirements can be a barrier for quick system setup or educational use. Here, we present Web-PackMol, a lightweight, zero-installation web application that employs a stochastic Monte Carlo approach for molecular packing. Web-PackMol allows users to pack complex molecules within arbitrary 3D regions defined by dual-constraint logic (e.g., inside a box AND outside a sphere). It includes built-in features such as real-time 3D visualization, automated density calculation on the generated systems, and session persistence through JSON exports. While algorithmically less efficient than PACKMOL (which stays the best choice to pack large, dense systems), Web-PackMol is far easier to use as it operates right in the web browser and through a regular graphical interface without scripting, while allowing to accomplish a vast majority of the most common procedures within seconds to minutes, as we demonstrate with examples similar to those presented in the PACKMOL paper plus some unique ones. Web-PackMol is available as a module of the online PDB manipulation suite at https://pdbms.altervista.org.