I'm writing my first MD simulation (ever) for liquid Argon. The code is up and running. I am supposed to do the calculations in the NVE ensemble. Having implemented a 4th order symplectic integrator (forest-ruth) the total energy of my system (approx 1000 atoms) oscillates (as expected).
Now I am "measuring" the heat capacity of my system, which I do by calculating the mean total energy and it's fluctuations for several distinct simulations (using the same parameters).
This is exactly the point that I don't get (conceptually). By definition, the total energy of a system is fixed in the microcanonical ensemble. Am I in the microcanonical or in the canonical ensemble when I do an MD simulation? The literature (I have) is somewhat sloppy when it comes to this.