In this paper we propose a new method of coarse-grained computer simulations of the microgel formation in course of free radical precipitation polymerization. For the first time, we simulate the precipitation polymerization process from a dilute solution of initial components to a final microgel particle with coarse grained molecular dynamics, and compare it to the experimental data. We expect that our simulation studies of PNIPA-like microgels will be able to elucidate the subject of nucleation and growth kinetics and to describe in detail the network topology and structure. Performed computer simulations help to determine the characteristic phases of the growth process and show the necessity of prolongated synthesis for the formation of stable microgel particles. We demonstrate the important role of dangling ends in microgels, which occupy as much as 50% of its molecular mass and have previously unattended influence on the swelling behavior. The verification of the model is made by the comparison of collapse curves and structure factors between simulated and experimental systems, and high quality matching is achieved. This work could help to open new horizons in studies that require the knowledge of detailed and realistic structures of the microgel networks.