A range of attributes of a molecular dynamics model for Ne-atoms colliding with a n-hexylthiolate self-assembled monolayer (SAM)/Au{111} surface are investigated to determine how they affect the energy-transfer dynamics. Explicit-atom (EA) and united-atom (UA) models for the SAM surface give similar energy accommodation, with energy transfer to the EA model approximately 10% less efficient. An accurate potential energy. function is needed to described the interaction between Ne and the carbon and hydrogen atoms of the SAM. Quasiclassical and molecular dynamics sampling of initial conditions for the SAM give very similar simulation results. A SAM model with only 35 alkyl chains gives the same energy transfer to the Ant I I I I substrate as do much larger models. Energy transfer to the Au{111} substrate is unimportant during the Ne-atom collision. Increasing the temperature of the SAM in the initial conditions and, thus, increasing the SAM's thermal motion lead to more energy dissipation pathways and broaden the energy-transfer distribution function As found in previous work, the apparent Boltzmann component in this distribution does not arise from a trapping desorption intermediate.