The Lennard-Jones sites and the electrostatic charges are created/annihilated in separate runs, which simplifies the use of fix adapt/fep and compute fep. The Lennard-Jones sites are handled using soft core potentials (pair lj/cut/soft). Trajectories are at constant NpT, so corrections for the fluctuating volume are included.

The following directories contain input files and results for calculations using free-energy perturbation (FEP):

mols -- molecule description files and force field database used to create the initial configuration used for the simulations data.lmp
fep01 -- Calculation using FEP, multi-stage creation of one SPC/E molecule, LJ and q. Results in fep01-lj.fep and fep01-lj.fep
fep10 -- Calculation using FEP, multi-stage deletion of one SPC/E molecule, q and LJ. Results in fep10-q.fep and fep10-lj.fep

The Python script fep.py found in the tools directory can be used to calculate the free-energy differences corresponding to the transformations above:

fep.py 300 < fep01-lj.fep

fep.py 300 < fep01-q.fep

fep.py 300 < fep10-q.fep

fep.py 300 < fep10-lj.fep

The outputs are in kcal/mol and can be compared with the experimental value of -6.3 kcal/mol, or with a simulation value from the literature of -6.7 kcal/mol Gonçalves, Stassen, Pure Appl Chem 76 (2004) 231.

These example calculations are for tutorial purposes only. The results may not be of research quality (not enough sampling, size of the step in lambda not optimized, etc.)