To study interaction between a single atom protrusion and molecules in a self-assembled monolayer during non-contact atomic force microscopy (nc-AFM), we attempted molecular dynamics (MD) simulation using a monolayer consisting of united CH3 atoms with a mass (m(0)). The interaction of a single gold atom tip with the united atoms and a continuum gold substrate was treated explicitly in terms of microscopic potentials under temperature control with Berendsen's thermostat. On the other hand, the probe tip with an artificial reduced mass of ca. 600m(0) was bound to a cantilever spring in order to measure its macroscopic nc-AFM behavior. Energy dissipation as a function of temperature was also studied. (C) 2003 Elsevier Science B.V. All rights reserved.