PACKMOL

Initial configurations for Molecular Dynamics Simulations by packing optimization

Institute of Chemistry and Institute of Mathematics
University of Campinas
Institute of Mathematics and Statistics
University of São Paulo

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Input examples

Download input files for all examples at once:
tar.gz file: examples.tar.gz
zip file: examples.zip

Both clean and commented input files can be used.

Important: If you are using Windows or DOS and you get some input/output error when using these files, open each file in the wordpad, save them as "txt" and try again.

These examples were run in a VAIO NR11Z/S laptop. Times may vary for similar problems depending on how hard is to find the packing solution.

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.