I've since found the source of my problem - the program was
measuring the (marginally shorter) distance across the PBC
boundary, rather than the distance
within the box. Unfortunately there doesn't seem to be a way to
turn PBC images off (correct me if I'm wrong?), so I guess I'm
going to do some jiggerypokery with the data and some math.
Use g_energy to output the box-Z then the distance you want should
be the box-Z minus the distance you get. This would be
super-dangerous unless you can be sure that it is actually
measuring the distance across the boundary each time. If, for
instance, it measures the distance you want one time and the
distance across the PBC the next time, then Mark's suggestion would
be the way to go.
I just realized that you could also use g_density, scripted to run
frame by frame if you need to, and average the histograms yourself.
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