Material characterization in nano-mechanical tests may provide information on the potential heterogeneity of mechanical properties. Here, we develop a robust neural-network interatomic potential (NNIP), and we provide a test for the example of molecular dynamics (MD) nanoindentation, and the case of body-centered cubic crystalline molybdenum (Mo). We employ a similarity measurement protocol, using standard local environment descriptors, to select ab initio configurations for the training dataset that capture the behavior of the indented sample. We find that it is critical to include generalized stacking fault (GSF) configurations, featuring a dumbbell self-interstitial on the surface, to capture dislocation cores, and also high-temperature configurations with frozen atom layers for the indenter tip contact. We develop a NNIP with distinct dislocation nucleation mechanisms, realistic generalized stacking fault energy (GSFE) curves, and an informative energy landscape for the atoms on the sample surface during nanoindentation. We compare our NNIP results with nanoindentation simulations, performed with three existing potentials – an embedded atom method (EAM) potential, a gaussian approximation potential (GAP), and a tabulated GAP (tabGAP) potential – that predict different dislocation nucleation mechanisms, and display the absence of essential information on the shear stress at the sample surface in the elastic region. Finally, we compared our NNIP nanoindentation results with experiments, showing reliable predictions for reduced Young’s modulus and observable slip traces. Display omitted