Packmol — упаковка молекул для MD-симуляций

★ 7.5 · general

packmol is a Claude Code skill that generates initial molecular configurations for MD simulations using Packmol, packing molecules into defined spatial regions to build liquid boxes, binary mixtures, solvated systems, and layered interfaces. It accepts input coordinates in PDB or XYZ format and supports rectangular and spherical constraints, exclusion zones, and fixed molecule placement with explicit position and orientation angles. The skill constructs a complete Packmol input file with parameters such as tolerance, number, inside box, inside sphere, outside sphere, and fixed, then executes packmol via a shell task. It is designed for researchers preparing starting structures before running LAMMPS ReaxFF or classical MD, particularly when a target density and overlap-free molecular environment are required.