This paper presents a detailed computational protocol for the atomistic simulation of formation and growth of metal-containing nanostructures during focused electron beam-induced deposition (FEBID). The protocol is based upon irradiation-driven molecular dynamics (IDMD), a novel and general methodology for computer simulations of irradiation-driven transformations of complex molecular systems by means of the advanced software packages MBN Explorer and MBN Studio. Atomistic simulations performed following the formulated protocol provide valuable insights into the fundamental mechanisms of electron-induced precursor fragmentation and the related mechanism of nanostructure formation and growth using FEBID, which are essential for the further advancement of FEBID-based nanofabrication. The developed computational methodology is general and applicable to different precursor molecules, substrate types, and irradiation regimes. The methodology can also be adjusted to simulate the nanostructure formation by other nanofabrication techniques using electron beams, such as direct electron beam lithography. In the present study, the methodology is applied to the IDMD simulation of the FEBID of Pt(PF3)4, a widely studied precursor molecule, on a SiO2 surface. The simulations reveal the processes driving the initial phase of nanostructure formation during FEBID, including the nucleation of Pt atoms and the formation of small metal clusters on the surface, followed by their aggregation and the formation of dendritic platinum nanostructures. The analysis of the simulation results provides spatially resolved relative metal content, height, and growth rate of the deposits, which represents valuable reference data for the experimental characterization of the nanostructures grown by FEBID.