Hi Matt,
Rolf is correct. The default ik differentiation PPPM conserves momentum but not energy. The ad differentiation that Rolf mentioned conserves energy but not momentum. My guess is that an orthogonal system would behave the same way as the triclinic system. You could test “kspace_modify diff ad” on an orthogonal system to see if you get better energy conservation. This diff ad option with PPPM is not yet available for triclinic systems but could be added if there was a compelling reason. Is there a reason you can’t just use a thermostat?
Stan