Calculation of free energy from potential and kinetic energy
The sum of the potential and kinetic energies is the internal energy, E (or U).
However, you don't necessarily need to know the entropy to calculate the free energy.  If you perform an equilibrium molecular dynamics simulation, you can derive the free energy from the equilibrium constant.
See, for instance:
https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21776
If you are modeling a constant T and V system, where there is no work done, the equilibrium constant would give you the Helmholtz free energy:
$$\Delta A = - R T ln K^{'}_{eq}$$
where A = E - TS
If you are modeling a constant T and p system, where you have no non-pV-work, the equilibrium constant would give you the Gibbs free energy:
$$\Delta G = - R T ln K^{''}_{eq}$$
where G = H - TS = E + pV - TS
The reason for this is that, at constant T and V, with no work term, minimizing A_sys corresponds to a maximization of S_univ, and thus determines the equilibrium condition. By contrast, at constant T and p, with pV-work only, minimizing G_sys corresponds to a maximization of S_univ, and thus determines the equilibrium condition.
I've marked the equilibrium constants as prime and double-prime to indicate that these would be numerically different.