Basic understanding of the structure and dynamics of materials and their response to external perturbations requires knowledge on the microscopic level, of the underlying energetics and atomic dynamics, whose consequences we observe and measure. Coupled with the above is the everlasting quest to observe and understand natural phenomena on refined microscopic scales, which provides the impetus for the development of experimental and theoretical techniques for the interrogation of materials with refined spatial and temporal resolution. In this paper we review molecular dynamics simulations for studies of the energetics and dynamical response of materials to external mechanical perturbations. Applications to investigations of solid and liquid interfacial systems under stress and to studies of the consequences of tip–substrate interactions in atomic force microscopy are demonstrated.