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.
tar -xvzf packmol.tar.gz cd packmol make
packmol < packmol.inp
virtualzx-nad/pypackmol is a decent Python wrapper for Packmol.
Alternatively I have been working on a wrapper myself which is still in development.