As a beginning, I am simulating Argon liquid at 94 K and characterising as it is done by the Rahman's first paper on Molecular Dynamics. After going through the first two chapters of Art of Molecular Dynamics by D. C. Rapaport, I got interested in calculating the entropy of the system at hand (using a technique outlined in that book). In his book, he has used the fact that H-function can be written as (apart from a constant factor) $$ H = \int f(\textbf v,t) \log f(\textbf v,t) d\textbf v $$
where $f(\textbf v,t)$ is the velocity distribution of the system at time $t$. Now as the simulation progresses, one should see that this $H$ function should increase with time (negative of entropy) as the system gets closer to equilibration and becomes a constant after it attains equilibration.
The main catch here is that, with a system that is not at the required temperature one has to scale the velocities for some time to achieve it. So because of this, I am not able to characterise or see this effective shift in H when I calculate and plot it. As it is seen in the image, the H-function drops to a low value and then raises again to reach a constant value.
My question is :