The site-selective deposition behavior of perylene onto a self-assembled monolayers (SAMs) patterned substrate was studied using the equilibrium and steered molecular dynamics simulations. Four kinds of different densely packed SAMs were constructed on silicon oxide substrates as the patterned templates. Equilibrium MD simulations showed that the packing density of alkyl chains on the substrate could influence the deposition behavior of the organic molecules. The potential of mean force (PMF) of the deposition process of perylene onto different density packed SAMs, which was calculated by the umbrella sampling with the weighted histogram analysis method (WHAM), determined the favorite location of perylene on the SAM. The equilibrium and non-equilibrium MD methods gave the same conclusion about the deposition positions of organic molecules on the patterned substrate. In summary, this comprehensive study is expected to provide useful information for the synthesis of new functional materials. (C) 2015 Elsevier B.V. All rights reserved.