In this work, we demonstrate the potential of combining state-of-the-art experimental and computational approaches, to overcome the limitations of each methods. This allows us to accurately capture and analyze the real-time atomic dynamics of Au NPs under experimentally relevant conditions. Our method begins with the acquisition high-resolution ADF-STEM images, which enable precise 3D reconstructions of the NP (through an iterative local minima search algorithm ). Specifically, we used 10 NP configurations each captured at 0.6 s intervals, during 6 s of ADF-STEM experimental data acquisition. These reconstructed NP structures serve as starting points for as many MD simulations, which then allow us to capture the real-time dynamics of NP. This approach enables us to run atomistic MD simulations relying on experimental-level sampling, studying the dynamics of Au NPs at different T and obtaining results in line with the experimental observations. Our analysis demonstrates that the dynamics we can reconstruct from MD simulations represent an equilibrium ensemble. Further, analyses based on SOAP and LENS allow us to elucidate the detailed dynamics within this ensemble. The level of insight that can be obtained with this combined experimental/computational approach provides us with a versatile tool to understand the real atomic-scale dynamics of metal NPs and to link this to their macroscopic properties.