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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See also:
ComplexMixtures.jl MDLovoFit
CellListMap.jl LovoAlign
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PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.

The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.

The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy.

The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.

See also:
ComplexMixtures.jl: A powerful package to understand solvation structures in complex solutions.
CellListMap.jl: Efficient and customizable cell list data structure for molecular simulations and customizable simulation analysis.