The effect of lipid modification on polyethylenimine (PEO-mediated DNA attraction was studied by performing umbrella sampling molecular dynamics simulations that involved PEIs modified with three different types of lipids: oleic acid (OA), linoleic acid (LA), and caprylic acid (CA). The potential of mean force between two DNA molecules in the presence of these lipid-modified PEIs was calculated using the weighted histogram analysis method, and it predicted the stability and size of the DNA aggregate. When compared to native PEI, lipid modification was found to enhance the stability of DNA aggregation in the case of long lipids (LA and OA) but reduce the stability in the case of a short lipid (CA). In addition, LA-substituted PEI was shown to form stronger DNA aggregate than OA-substituted PEI, which correlates positively with previous experimental observations.