Identified source of thermostat bug.

Multiple N-H chains are, for the moment, disabled. The dual thermostat
in CHARMM does not use multiple chains, so this may or may not be
re-enabled in the future.  The code I wrote supports multiple chains,
but there is a bug somewhere in it, so for now, disabling.

Change-Id: Ie12c557ed2daa29c06039c1eea1d44b3a5a3a64f