You have now calculated the free energy change for a simple transformation that has previously been calculated with high precision, the decoupling of van der Waals interactions between a simple solute (uncharged methane) and solvent (water). Hopefully this tutorial will provide you with the understanding necessary to take on more complex systems.

If you have suggestions for improving this tutorial, if you notice a mistake, or if anything is otherwise unclear, please feel free to email me. Please note: this is not an invitation to email me for GROMACS problems. I do not advertise myself as a private tutor or personal help service. That's what the GROMACS User Forum is for. I may help you there, but only in the context of providing service to the community as a whole, not just the end user.

Happy simulating!