wham [P|Ppi|Pval] hist_min hist_max num_bins tol temperature numpad \
metadatafile freefile [num_MC_trials randSeed]
The first (optional) argument specifies the periodicity of the reaction coordinate. For a nonperiodic reaction coordinate (a distance, for example), it should be left out. ``P'' means that the reaction coordinate has a periodicity of 360, appropriate for angles. ``Ppi'' specifies a periodicity of 2*pi, appropriate for angles measured in radians. ``Pval'' specifies periodicty of some arbitrary amount, val, which should be an integer or floating point number. For example, ``P180.0'' would be appropriate for an angle with twofold symmetry.
hist_min and hist_max specify the boundaries of the histogram. As a rule, all data points outside the range (hist_min, hist_max) are silently ignored. The only exception is that if an entire trajectory is outside the range, the program halts with an error message. The solution is to remove that file from the metadata file. hist_min and hist_max should be floating point numbers.
num_bins specifies the number of bins in the histogram, and as a result the number of points in the final PMF. It should be an integer.
tol is the convergence tolerance for the WHAM calculations. Specifically,
the WHAM iteration is considered to be converged when no 
value for any
simulation window changes by more than tol on consecutive iterations. As
the program runs, it prints the average change in the F values for the most
recent iteration. Obviously, this number will be smaller than tol
before the computation converges, because convergence is triggered by the
largest change as opposed to the average.
temperature is a floating point number representing the temperature in Kelvin at which the weighted histogram calculation is performed. This does not have to be the temperature at which the simulations were performed (see below for discussion).
numpad specifies the number of ``padding'' values that should be printed for periodic PMFs. This number should be set to 0 for aperiodic reaction coordinates. It doesn't actually affect the calculation in any way. Rather, it just alters the final printout of the free energy, to make plotting of periodic reaction coordinates simpler. This is more important for wham-2d than wham.
metadatafile specifies the name of the metadata file. The format of this file is described below.
freefile is the name used for the file containing the final PMF and probability distribution.
num_MC_trials and randSeed are both related to the performance of Monte Carlo bootstrap error analysis. If these values are not supplied, error analysis is not performed. num_MC_trials should be an integer specifying the number of fake data sets which should be generated. randSeed is an integer which controls the random number seed - the value you pick should be irrelevant, but I let the user set it primarily for debugging purposes.