The purpose of this tutorial is to guide the user through the process of building a heterogeneous biphasic system composed of hydrophobic (cyclohexane) and hydrophilic (water) layers. Several other types of systems will be discussed. The scope of the tutorial is simply in building these systems. Details will not be given for simulation methodology, as there are numerous other tutorials that describe such workflows.

This tutorial is designed to be compatible with any GROMACS version higher than 4.5.