We begin by copying the file setup.pgn from the example output folder to e2e_01.inp.
Then

module load namd

psfgen e2e_01.inp > e2e_01.out

This creates setup.psf and setup.pdb.

Copy setup.pdb to zero.fep and edit the last numeric column to define which parts
of the ethane structure are to be modified.

The backward-noshift.namd and forward-noshift.namd files are input files (not using our
strategy of numerical file names) that demonstrate the hazards of endpoint effects on
the FEP method.  
The free energy profiles are in the .fepout files:

grep change backward-noshift.fepout |awk '{print $9,$19}' > backward-noshift.ene

will take the two relevant columns and put them in a new file.

The backward-shift.namd and forward-shift.namd files provide a better solution.
