To make sure that the pushing speed was slow enough such that ligand molecules had enough time to relax, simulations were repeated with half the pushing speed. In addition, simulations were performed without pushing or fixing atoms with an isothermal-isobaric (NPT) ensemble (see Supporting Information, Section S2.3.4). In both cases, no significant deviation of the average preferred surface-to-surface distances from the ones obtained by the standard simulation protocol was observed (12.0 ± 0.7 Å with half the pushing speed, 11.7 ± 0.4 Å with the NPT ensemble, and 12.0 ± 0.4 Å with the standard protocol), showing that the surface-to-surface distance does not depend on our simulation protocol. We decided to use the pushing protocol as standard protocol for this work instead of NPT simulations, as it can directly be applied to analyze strain sensing properties of GNP assemblies in the future.