packmollisted

# Packmol Skill Build initial configurations for molecular dynamics simulations using Packmol. ## What is Packmol? Packmol creates initial configurations for MD simulations by packing molecules according to spatial constraints. It places molecules in boxes, around proteins, at interfaces, or within complex geometries (spheres, cylinders, ellipsoids) while ensuring no overlaps. ## Installation Install Packmol via pip: ```bash pip install packmol ``` Verify installation: ```bash packmol -h ``` For more installation options, see the [Packmol website](https://m3g.github.io/packmol/). ## Quick Start ### Basic Box Packing Create a simple box of water molecules: ```text # water_box.inp tolerance 2.0 filetype pdb output water_box.pdb structure water.pdb number 1000 inside box 0. 0. 0. 40. 40. 40. end structure ``` Run Packmol: ```bash packmol < water_box.inp ``` ### Solvate a Protein Solvate a protein with water and ions: ```text # solvation.inp tolerance 2.0 filetype pdb output solvated.pdb structure protein.pdb number 1 fixed 0. 0. 0. 0. 0. 0. center end structure structure water.pdb number 5000 inside box -10. -10. -10. 50. 50. 50. end structure structure SOD.pdb number 10 inside box -10. -10. -10. 50. 50. 50. end structure structure CLA.pdb number 10 inside box -10. -10. -10. 50. 50. 50. end structure ``` ### Liquid-Liquid Interface Build a water/chloroform interface: ```text # interface.inp tolerance 2.0 filetype pdb output interfa