:::bash
~/$DIR/src/liquid.sims/generate.liq.sh mol.top mol.pdb mol.par Nmols L_size

:::text
mol.top: CHARMM-compatible topology file
mol.pdb: PDB file of the compound alone
mol.par: CHARMM-compatible parameter file
Nmols: Number of molecules requested in the pure-liquid box
L_size: Size requested for the pure-liquid box

The script will use packmol to generate Nmols molecules in a box of size L_size. You must estimate the two numbers to get a reasonable starting density. Packing too many molecules in a box will prevent the script from completing.

The script will provide the files pureliquid.psf, pureliquid.crd, and box.size. Make sure everything looks okay by inspecting the conformation in, e.g., VMD.