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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See also:
ComplexMixtures.jl MDLovoFit
CellListMap.jl LovoAlign
The TANGO project
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JM Home-Page
EGB Home-Page
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Input examples

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

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
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:
Output file:
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
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
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
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.