Packmol

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.

• Open Babel website
• Packmol GitHub repository
• Packmol paper

Installation

The official user guide for Packmol does a really good job of explaining how to install and use Packmol. Basically, you need to download Packmol here. Unpack the tar file and compile:

tar -xvzf packmol.tar.gz

cd packmol
make

Running packmol

packmol < packmol.inp

Python wrapper

virtualzx-nad/pypackmol is a decent Python wrapper for Packmol.

Alternatively I have been working on a wrapper myself which is still in development. See packmol.py here