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lammps/examples/USER/fep/CH4hyd/README.md
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Free Energy of Hydration of Methane
===================================
Example calculation of the free energy of hydration of methane with
LAMMPS using *compute fep* and *fix adapt*.
Methane is represented by the 5-site OPLS-AA model (1 molecule). Water
is represented by the 4-site TIP4P-Ew model (360 molecules). Interactions
of sites that are being created or deleted are treated using soft-core
verions of the Lennard-Jones and Coulomb potentials (*pair
lj/cut/coul/long/soft*) in order to avoid singularities.
The following directories contain input files and results for
calculations using free-energy perturbation (FEP) and
finite-difference thermodynamic integration (FDTI):
* `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 a methane
molecule. Results in `fep01.lmp`
* `fep10` -- Calculation using FEP, multi-stage deletion of a methane
molecule. Results in `fep10.lmp`
* `fdti01` -- Calculation using TI/FDTI, creation of a methane
molecule. Results in `fdti01.lmp`
* `fdti10` -- Calculation using TI/FDTI, deletion a methane
molecule. Results in `fdti10.lmp`
The free-energy profiles can be observed by plotting the values in the
third column of the results files. The Python scripts `fep.py`,
`nti.py` and `fdti.py` found in the `tools` directory can be used to
calculate the free-energy differences corresponding to the above
transformations:
fep.py 300 < fep01.lmp
fep.py 300 < fep10.lmp
nti.py 300 0.002 < fdti01.lmp
nti.py 300 0.002 < fdti10.lmp
fdti.py 300 0.002 < fdti01.lmp
fdti.py 300 0.002 < fdti10.lmp
The outputs are in kcal/mol and can be compared with the experimental
value of 2.0 kcal/mol, or with a simulation value from the literature
obtained with the same force field models used here: 2.27 kcal/mol
[MR Shirts, VS Pande, J Chem Phys 122 (2005) 134508].
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 or of the delta for numerical derivative not optimized, no
evaluation of ideal-gas contributions, etc.)
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