With the aim of designing an efficient procedure for producing biocompatible drug delivery systems based on nanoparticle carriers for in situ controlled antibiotic release, we have defined a novel computational approach resorting to a reactive force field capable of realistically describing hybrid systems. The modeling procedure was focused on well-known components, namely gold nanoparticles, citrate, chitosan and gentamicin, and the experiments tuned on purpose. On the one hand, gold nanoparticles were synthesized, fuctionalized with chitosan, loaded with gentamicin and characterized by means of transmission electron microscopy (TEM), scanning electron microscopy (SEM), dynamic light scattering (DLS), UV-visible (UV-vis) spectroscopy, and Fourier transform infrared spectroscopy (FTIR). On the other hand, an effective model of a functionalized gold nanoparticle was created and its structure and dynamics were explored by classical reactive molecular dynamics simulations in solution based on the ReaxFF atomistic description. The structure, dynamics and drug release were reproduced realistically disclosing the motion of all the molecular components, their adsorption on the metal support, desorption, intermolecular interactions and self-assembly. The system size was very close to the experimental conditions and all the calculations could efficiently identify the most probable binding modes, the locations of the adsorbed molecules, the characteristic arrangements of the chains and the effects due to the surrounding environment. The role played by the substrate and water molecules in the releasing process was described in detail. In line with the literature it was found that the antibiotic activity was preserved and the drug release from the carrier could be tuned by changing the chitosan/getamicin weight ratio and the deposition pattern of the adsorbed layers.