Mechanical properties of nanoscale objects can be measured with an atomic force microscope (AFM) tip. However, the continuum models typically used to relate the force measured at a certain indentation depth to quantities such as the elastic modulus, may not be valid at such small scales, where the details of atomistic processes need to be taken into account. On the other hand, molecular dynamics (MD) simulations of nanoindentation, which can offer understanding at an atomistic level, are often performed on systems much smaller than the ones studied experimentally. Here, we present large scale MD simulations of the nanoindentation of single crystal and penta-twinned gold nanorod samples on a silicon substrate, with a spherical diamond AFM tip apex. Both the sample and tip sizes and geometries match commercially available products, potentially linking simulation and experiment. Different deformation mechanisms, involving the creation, migration and annihilation of dislocations are observed depending on the nanorod crystallographic structure and orientation. Using the Oliver-Pharr method, the Young's moduli of the (100) terminated and (110) terminated single crystal nanorods, and the penta-twinned nanorod, have been determined to be 103 ± 2, 140 ± 4 and 108 ± 2 GPa, respectively, which is in good agreement with bending experiments performed on nanowires.