The ability to simulate surface-enhanced Raman scattering (SERS) is a vital tool in elucidating the chemistry of molecules near the vicinity of plasmonic metal nanoparticles. However, typical methods do not include the dynamics of the molecule(s) of interest and are often limited to a single or few molecules. In this work, we combine molecular dynamics simulations with the dressed-tensor formalism to simulate the SERS spectra of Ag nanoparticles coated with a full monolayer of pyridine molecules. This method allows us to simulate the ensemble-averaged SERS spectra of more realistic large scale systems, while accounting for the organization of molecules in the hotspots. Through these simulations, we find that the preferential binding location and orientation of the molecules, the choice of electrodynamics method, and the inclusion of field gradient effects influence both the enhancement distribution and the spectral signatures. We also show that both the translational and rotational motions of a pyridine molecule near a nanoparticle junction may be effectively tracked through its SERS spectrum.