The examples below illustrate the use of compute fep, fix adapt/fep and pair lj/cut/coul/long/soft to calculate free energy differences. They present just one version of many possible ways of constructing a path from the initial to the final states.

CH4hyd -- free energy of hydration of methane (simple). FEP and FDTI methods.
SPCEhyd -- free energy of hydration of SPCE water (simple). FEP in separate steps for the LJ sites and the atomic charges.
CH4-CF4 -- free energy difference of transforming methane into perfluoromethane, in water (quite simple). FEP and BAR methods.
CC-CO -- hydration free energy difference between ethane and methanol (a bit more complex). FEP method.
C7inEthanol -- insertion / deletion of a hexane molecule in ethanol. The hexane is described by the lj/class2/coul/long/soft potential.
quicktests -- very short runs with charged Lennard-Jones atoms to test compute fep, fix adapt/fep and pair lj/cut/coul/long/soft.