Indentation is one of the most widely used methods to determine the characteristics of metallic materials. Molecular dynamics (MD) simulations are a powerful tool to investigate the material behavior at the atomistic scale during nanoindentation and to get insights into the understanding of the plastic deformation of a material. However, the optimal choice of parameters for the simulation is not clear, and there is a large body of literature with strongly different simulation configurations. In this study, we systematically investigate the effect of the choice of interaction potentials, substrate size, indenter size and indentation velocity on hardness and defect generation during nanoindentation of face-centered cubic and body-centered cubic materials. As prototypical materials we consider aluminum and iron single crystals. Our sensitivity analysis reveals that the thickness of the substrate has a large influence on the measured hardness by MD simulations, while the impact of the indentation velocity is small. The results are useful for researchers planning to use MD to study the nanoindentation process using highly expensive potentials such as ReaxFF and COMB3 or small indenter velocities. This article aims to provide a guideline for designing nanoindentation simulations using MD.