Use of periodic boundary conditions only changes one thing in the
code: when calculating the biasing potential from a simulation window for a
specific bin in the histogram (the values in Equation 8 of Roux's
paper, cited above), the minimum image convention is applied. Thus, for a
window with the biasing potential centered at 175 degrees, the ``distance''
to the bin at -175 is 10 degrees, not 350 degrees.
The numpad argument on the command line is useful primarily for periodic reaction coordinates. It specifies a number of additional windows to be prepended and appended to the final output, such that the periodicity is explicitly visible in the free energy. So, if a calculation was done using 360 degree periodicity, 36 windows, with the reaction coordinate ranging -180 to 180, and numpad=5, a total of 46 values would be output, from -225 to +225. The numpad value has no effect at all on the values computed for the PMF and probability.