The fastest solution to poor scaling of the computeSwapMatrix routine with
replica size turns out to be parallel multiprocessing of the replica
coordinates. This is a bit of a chore with Python in general, and the
implementation here is a bit confusing due to the need to be able to
pickle/import the task being parallelyzed. However, this is probably how a
kludgy implementation of the "shell script" option would look also and for a
similar reason. That option will be more generalizeable than this one, but
suffers from a number of problems related to inheriting environmental
variables, etc.

In the end I was just able to mock up, test, and debug this way much faster.