This tutorial will guide the user through the process of calculating a simple free energy change, the decoupling (i.e. removal) of van der Waals interactions between neutral methane and a box of water. It is an updated version of the same tutorial written by David Mobley that I found extremely useful. Due to a substantial number of code changes between the GROMACS version used therein (3.3.1) and present versions (including differences in topology handling and data analysis), I think it poignant to provide an updated workflow here.

This tutorial requires a GROMACS version in the 4.5.x or 4.6.x series. Any version prior to 4.5 will not work.