Several characteristics of heavy-ion reactions at intermediate energies, such as the formation of an intermediate residue, or neck-like structure, are not well understood. To study this and other features of heavy-ion collisions and their fragmentation, a semi-classical model based on the use of molecular dynamics is presented. The model uses a two-body potential developed to reproduce nucleon-nucleon cross sections realistically. Preliminary results of the use of the model to study the caloric curve of nuclear matter, formation of necks, as well as the temperature evolution of the system are discussed.