The actual partition function is unimaginably formidable. For just $N$ point particles in a 3D box, it's already got $3N$ dimensions. If the box is length $L$, GROMACS would probably divide the box into a machine-precision grid and calculate the energy from $\sim L \times 10^{10}$ values in each dimension. The partition function would incorporate all of that information, the energy at each of those $L \times 10^{30N}$ points; even for two particles in a one unit box, that's already $10^{60}$.
When you speak of "the partition function" you're talking about the entire thermodynamic state of the system and all of its possible permutations. If we truly knew that function, we would be omniscient and could calculate anything about the system! Since we can't really calculate at the level of the entire partition function, we use simulations (MC and MD, etc.) to sample regions of interest (usually low-energy areas).
To a computational chemist, the partition function is most practical for its mathematical basis. It's the way to get from statistical mechanics (a bunch of particles moving around in a box) to actual thermodynamic properties (Helmholtz energy, pressure, etc.).
As a practical example, imagine you want to calculate the surface tension for some fluid interacting according to some potential function. Using LAMMPS or GROMACS, you can set up your vapor-liquid interface in the simulation box. Then by simply changing (perturbing) the simulation box shape and measuring the energy change, you can calculate the surface tension. The whole derivation of this method starts with the configuration integral of the partition function and then, via mathematical manipulation, eventually leads to the quantity we want to calculate and variables we can actually measure.
Test-area method - Gloor and Jackson, J. Chem. Phys. 123, 134703 (2005)
Free energy perturbation - Zwanzig, J. Chem. Phys. 22, 1420 (1954)
