Chemoepitaxial guidance of block copolymer (BCP) directed self-assembly (DSA) in thin films is explored. The underlayers studied are line-space patterns composed of repeating highly preferential pinning stripes separated by larger, more neutral, background regions. Studies have shown that varying the properties of such a chemical pattern can have a large effect on processing window, but the effect of changing the chemical pattern on many properties of interest such as footing of the BCP are hard to measure experimentally. This study uses a coarse-grained molecular dynamics model to study a 2x density multiplying underlayer by varying the pinning stripe width and background region chemical interactions and analyzing the effect on self-assembled BCP lines. Decreasing pinning stripe width or making the background region more neutral is found to increase the LER of the lines. An undersized pinning stripe width with a neutral background region is found to give the straightest sidewalls for the formed lines, while a larger pinning stripe causes the pinned line to foot (expand near the substrate) and a preferential background region causes the unpinned line to undercut (contract near the substrate). A simple model was developed to predict the optimal conditions to eliminate footing. Using this model, conditions are found that decrease footing of the pinned line but these conditions increase undercutting in the unpinned line. Deformations in either the pinned or unpinned line propagate to the other line. There exists a tradeoff between LER and the footing/undercutting, that is, decreasing LER increases footing/undercutting and vice versa.