The protocols used to equilibrate pressure and temperature in "run.in.npt"
as well as "run.in.nvt" have not been carefully tested.  You will have to
run a short simulation to confirm that the system has the correct energy
and volume for a system under these conditions.  (It might help to create a
version of TIP5P water with very stiff springs which does not rely on
"fix rigid" which can be simulated together with ethanol using a suitably
small timestep.  I apologize that we have not done this step for you already.)

Also: These protocols have also not been tested for efficiency.  Specifically,
the flexible ethanol and rigid TIP5P molecules may diffuse at vastly different
rates due to the fact that different computer code is used to integrate their
equations of motion.

Please send corrections or suggestions to jewett.aij -at- gmail dot com
(and/or submit a pull-request).
