This study performs molecular dynamics simulations in order to clarify the atomic-scale stick-slip behaviour commonly observed when performing surface measurements using an atomic force microscope (AFM). In investigating the surface effects of adhesion, contact deformation, nanoindentation and fracture which occur when a diamond tip interacts with a copper surface, this study considers that both the substrate and the tip deform. The theoretically predicted dynamic behaviour of the AFM cantilever tip includes tip oscillation and noise induced by adhesion, nanoindentation and fracture effects. Molecular dynamics simulations are performed to clarify the atomic-scale friction mechanisms associated with surface deformation and to investigate the dynamic behaviour of the tip during AFM surface measurement. The relative influences of the adhesion, nanoindentation and fracture effects upon the stick-slip phenomenon are investigated.