Research of the mechanisms of interactions between nanoparticles (NPs) and lipid bilayers (LBs), which constitute the foundation of cell membranes, is important in order to understand not only the specifics of NP drug delivery and imaging but also to understand the harmful effects related to NP toxicity. In this work, a coarse-grained molecular dynamics (CGMD) with implicit solvent is used to elucidate the stability of LBs supported on silica substrates decorated with hydrophilic and hydrophobic NPs. We reproduce the experimental observation that large NP (>22 nm) can be coated by stable LBs, while smaller NPs (<22 nm) induces holes in the membrane. This result was achieved due to introducing novel features in CGMD set-up, which (a) secure the isotention membrane condition and (b) account for long-range lipid-substrate interactions due to the existence of the nanometer thick hydration layers between LB and silica. The latter effect is incorporated by using the effective long-range potential of interactions between lipid heads and silica mimicking the disjoining pressure developed in the hydration layer. The proposed GCMD method allowed for simulation of large systems with up to 40 nm NPs in the simulation cell of 231 ∗ 154 ∗ 77 [Special character(s) omitted] in volume. The method can be extended and applied to other NP-membrane systems, specifically to study the membrane stability affected by the presence of host bodies.