Single-walled carbon nanotubes (SWNTs) wrapped with different types of lipids and polyethylene glycol (PEG)-grafted lipids were simulated with lipid bilayers. Simulations were carried out with the previously parametrized coarse-grained (CG) SWNT and PEG force fields that had captured the experimentally observed conformations of self-assembled SWNT lipid complexes and phase behavior of PEG-grafted lipids. Simulations of multiple copies of the SWNT in water show that all pure SWNTs aggregate, lipid-wrapped SWNTs partially aggregate, but those wrapped with lipids grafted to PEG (M-w = 550) completely disperse, indicating the effect of short PEG chains on interparticle aggregation, in agreement with experiment. Starting with initial SWNT orientation parallel to the bilayer surface, SWNTs wrapped with lysophospholipids and PEG (M-w = 550)-grafted lipids insert into the hydrophobic region of the bilayer, while SWNTs wrapped with phospholipids and longer PEG (M-w = 2000)-grafted lipids do not. These indicate that SWNTs insert because of the hydrophobic interaction with the bilayer tails, but the tight wrapping of charged lipid headgroups and long hydrophilic PEG chains can weaken the hydrophobic interaction and inhibit SWNT insertion. The inserted SWNTs contact the entire tails of neighboring lipids in one leaflet of the bilayer, which disorders the lipid bilayer and induces positive curvature. Our findings indicate that interparticle aggregation, SWNT penetration, and membrane curvature can be modulated by the SWNT-lipid structure and the PEG length.