Single molecule surface enhanced Raman spectroscopy (SM-SERS) sees spikes in the intensity of the signal which has been attributed to hotspots and picocavities where intense localized electromagnetic fields can be found. Recently, it has been shown that substrate reconstruction is linked to the formation of hotspot and picocavities indicating that the SERS substrates are not as static as previously perceived. In this paper we use DFTB+ to simulate picocavities in order to explore the factors that affect the substrate dynamics. The simulations were run using two hemispheres made of gold that were either 8, 9, or 10 Å in radius that were placed at varying distances from 3.0-10 Å with either 2, 4, or 6 thiols placed between the two hemispheres. Each system was run at 300 or 500 K. Through over a 100 different simulations temperature and adsorbate density were the biggest contributing factors to substrate reorganization. The two factors worked concurrently to create nanostructures on the surface of the gold SERS substrate that was simulated. Higher temperatures caused the substrate to reorganize at a faster rate but also increased the extent to which the substrate would reorganize. Adsorbate molecules would pull up certain atoms to create adatoms, with an increased density of adsorbate molecules adatoms and nanostructures would form more frequently. Distance between the two gold surfaces affected solely the ability of adatoms from one surface to be transferred to the other surface. During the simulations it was also observed there was a drive to reach a stable equilibrium structure which could be mitigated with increased temperature and adsorbate density due to creating a shallower potential energy surface (PES) on the substrates. These simulations demonstrate the dynamic nature of SERS substrate and the advantage of using simulations in order to study these anomalies.