This example will show you how to use Music to run a simulation of flexible butane molecules in the zeolite silicalite. We consider specifically n-butane, which is a 4-carbon straight-chain alkane. In terms of the united atom model, butane is composed of 2 methyl atoms and 2 methylene atoms. The butane molecule is fully flexible, and we use potential models to describe the bond stretching, bond bending, and torsion angles in the molecule. Interactions between the butane molecules are described by a 12-6 Lennard-Jones potential.
The zeolite, silicalite, has a 3-dimensional pore structure. Typically, the pores are classified as either zig-zag, straight, or intersections where the zig-zag and straight meet. When calculating the zeolite-butane interactions, we only consider interactions between the zeolite lattice oxygen atoms and the butane molecules. Furthermore, we will use a rigid zeolite lattice.
Some of the input files and output files are listed below.