The article covers the computational framework providing an insight on vapour phase coagulation of nanoparticles synthesized by atmospheric pressure PECVD in an RF capacitive discharge. The proposed model is based on the solution of motion equations for neutral and charged nanoparticles in the plasma downstream area featuring a nonuniform distribution of electric potential. Within the model particles collisions are accounted by an O'Rourke derived stochastic method, reduction of computational time is attained by division of the nanoparticle stack into parcels. We argue that nanoparticles are mainly synthesized in the plasma downstream area. Size distribution of the particles is governed by their uneven motion in the nonuniform electric field. We demonstrate that particles of tens of nanometer in diameter result from coagulation of neutral nanoparticles, whereas the larger nanoparticles result from coagulation of charged particles. The model shows that charged particles trapped in the potential well in the vicinity of the discharge electrode grow up to micron size. The proposed model is validated by the experimental results of silicon dioxide nanoparticles synthesis; it may be extended to a vast range of materials provided certain modifications of the particles motion equations are done. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)