Script: alchemical-gromacs.py

An illustration of MBAR applied to alchemical free energy
calculations, and comparison of MBAR to a number of other free energy
methods described in Paliwal and Shirts, J. Chem. Theory Comp, v. 7,
4115-4134 (2011).

The dataset contained in the data/ directory is obtained from a series
of alchemical intermediates for computing the hydration free energy of
3-methylindole using a beta version of Gromacs 4.6.  3-methylindole is
represented by its OPLS parameters and water by TIP3P.  The paramters
are from Shirts and Pande. J. Chem. Phys. 122, 134508 (2005).

Electronic and van der Waals interactions are turned off in the same
simulation, over 38 total states.  Files used to generate the data are
included in the directory inputfiles/3-methylindole-38steps. The
placeholder FEP_STATE is replaced with the integer 0 to 37 to produce
the 38 input files.

To run the files for a sparser lambda spacing (11 total states),
invoke specifying the data directory to use with the command:

python alchemical-gromacs.py -d data/3-methylindole-11steps -p dhdl -t 298

For the denser lambda spacing with 38 total states, run
python alchemical-gromacs.py -d data/3-methylindole-38steps -p dhdl -t 298

Note that all these files were generated in gromacs with calc-lambda-neighbors = -1, where one calculates 
the energy at all the other states.

One can also run alchemical-gromacs.py on files that include just the
states that are +1/-1 states from the intermediate simulated at.
MBAR, however, cannot be run on this restricted data set.  The
difference between these two files is automatically recognized.  For
an example, try:

python alchemical-gromacs.py -d data/3-methylindole-11steps-neighbors -p dhdl -t 298

Note how all the output results are the same EXCEPT for MBAR, which
must be omitted from the calculation.

Sample output for both cases is provided in the files:
alchemical-gromacs.py_output_11steps
alchemical-gromacs.py_output_38steps
alchemical-gromacs.py_output_11steps_neighbors

Help for alchemical_gromacs.py (obtained with 'python alchemical_gromacs.py') is:

Options:
  -h, --help            show this help message and exit
  -d DIR, --dir=DIR     Directory in which data files are stored. Default:
                        Current dir.
  -f, --forwrev         Plotting the free energy change as a function of time
                        in both directions. Default: False.
  -p PREFIX, --prefix=PREFIX
                        Prefix for datafile sets, i.e. prod (default).
  -s EQUILTIME, --skiptime=EQUILTIME
                        Discard data prior to this specified time as
                        'equilibration' data. Units picoseconds. Default: 100
                        ps.
  -t TEMPERATURE, --temperature=TEMPERATURE
                        Temperature in K. Default: 298 K.
  -v, --verbose         Verbose option for BAR and MBAR. Default: False.
  -u UNITS, --units=UNITS
                        Units to report energies, 'kJ' vs. 'kcal'. Default: kJ