We use molecular dynamics simulations at the atomistic level to build a model of aromatic polyamide polymer used in reverse osmosis membranes, from a mixture of m-phenylene diamine (MPD) and trimesoyl chloride monomers (TMC). Our purpose is to use different MPD to TMC ratios to reproduce the compositional depth-dependence observed experimentally during interfacial polymerization. MPD to TMC ratios in the range 1:4 to 5:1 have been employed. Reproducibility of the polymerization algorithm is thoroughly studied through the building of several samples under identical conditions. We notice that simulation time of a few microseconds are necessary in order to reach equilibration. We show that the initial monomer ratio has a strong influence onto the final polymer composition and different chemical structures have been created. Large differences are seen concerning cross-linking degree and remaining un-reacted groups. Comparison with available experimental data show that samples built using intermediate values of the MDP to TMC ratio closely resemble aromatic polyamide membranes. We conclude that the simulated samples created under different local concentrations can describe properly the chemical heterogeneities observed experimentally in reverse osmosis membranes.