Improved thermostat propagation.

Thermostat positions need to be updated at a specific point during
relative velocity scaling.  This commit updates the NHC_trotter
function to conditionally update thermostat positions (TRUE for all
cases that are not Drude simulations).  Otherwise, the relative
scaling algorithm handles the position updates.

Change-Id: I6e0adb1684609be49aa5e27c125fe0c8252e4568