freebsd-ports/science/packmol/pkg-descr

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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 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.