PACKMOL

Input examples

Simple mixture of water and urea	[Click on the Images]
Commented input file: mixture-comment.inp Clean input file: mixture.inp Molecules needed: water.pdb urea.pdb Output file: mixture.pdb Running time: 5 seconds Number of atoms: 6200 Number of molecules: 1400 Number of variables: 8400
Hormone in an interface of water and chloroform
Commented input file: interface-comment.inp Clean input file: interface.inp Molecules needed: water.xyz chlor.xyz t3.xyz Output file: interface.xyz Running time: 2.1 seconds Number of atoms: 4087 Number of molecules: 1219 Number of variables: 7308
Lipid bilayer with water over and below
Commented input file: bilayer-comment.inp Clean input file: bilayer.inp Alternative input file using different constraints: bilayer2.inp Molecules needed: palmitoil.pdb water.pdb Output file: bilayer.pdb Running time: 26 seconds Number of atoms: 7200 Number of molecules: 1100 Number of variables: 6600
Double layered spherical vesicle with water inside and outside
Commented input file: spherical-comment.inp Clean input file: spherical.inp Molecules needed: palmitoil.pdb water.pdb Output file: spherical.pdb Running time: 3 minutes Number of atoms: 69912 Number of molecules: 18234 Number of variables: 109404
4246 atom protein spherically solvated by water and ions.
Commented input file: solvprotein-comment.inp Clean input file: solvprotein.inp Molecules needed: protein.pdb water.pdb CLA.pdb SOD.pdb Output file: solvprotein.pdb Running time: 39 seconds Number of atoms: 53796 Number of molecules: 16551 Number of variables: 99300	Reference: Martínez L., et al. J. Med. Chem. 49 (1) 23-26, 2006.