The executable takes only one argument, the name of the input script. If not
given, it will default to "in.amideI". Each line of the input script begins
with a keyword followed by its value. An example is given here in "in.amideI".
The following keywords must be specified:
trajFile: Name of the xtc file to read the trajectory from
groFile:  Name of the gro file to read the configuration from
itpFile:  Name of an itp file to read charges and charge groups from,
	  multiple itp files can be specified with separate itpFile keywords
residue:  Which residues to label specified as a 3 letter amino acid code
	  followed by residue number (e.g. THR 75). If that residue appears
	  on multiple protein chains, each one will be labelled. Like itpFile
	  the residue keyword can be specified several times to label several
	  residues.

The following keywords are optional:
energyFile:  Name of output file with hamiltonian. Defaults to "Energy.txt"
dipoleFile:  Name of output file with dipoles. Defaults to "Dipole.txt"
energyRef:   Name of file with hamiltonian to compare to. If not supplied, no
	     comparison is done.
energyDiff:  If energyRef is specified, this gives the name of the output file
	     to print the hamiltonian comparison to. Defaults
	     to "Energy_diff.txt"
dipoleRef:   Name of the file with the dipoles to compare to. If not supplied,
	     no comparison is done.
dipoleDiff:  If diopleRef is specified, this gives the name of the output file
	     to print the dipole comparison to. Defaults to "Dipole_diff.txt"

The map parameters, including the electric field cutoff, can only be modified by
changing the source code. Start by looking in calcFreq.h in the section labelled
"Map parameters"