The inclusion of sophisticated density-dependent electronic stopping and electron-phonon coupling calculated with first-principles methods into molecular dynamics simulations of collision cascades has recently become possible thanks to the development of the so-called electron-phonon (EPH) model. This paper aims at employing the EPH model in molecular dynamics simulations of collision cascades in Si. In this context, the electronic stopping power is investigated in Si at low energies with Ehrenfest dynamics calculations. Also, the parametrization of the EPH model for Si, from first-principles Ehrenfest dynamics simulations to actual molecular dynamics simulations of collision cascades is performed and detailed. We demonstrate that the EPH model is able to reproduce very closely the density-dependent features of the energy lost to electrons obtained with ab initio calculations. Molecular dynamics collision cascade simulations results obtained in Si using the EPH model and the simpler but widely employed two-temperature model are compared, showing important discrepancies in the collision cascades results obtained depending on the model employed.