We present LUNES, an agent-based Large Unstructured NEtwork Simulator, which allows to simulate complex networks composed of a high number of nodes. LUNES is modular, since it splits the three phases of network topology creation, protocol simulation and performance evaluation. This permits to easily integrate external software tools into the main software architecture. The simulation of the interaction protocols among network nodes is performed via a simulation middleware that supports both the sequential and the parallel/distributed simulation approaches. In the latter case, a specific mechanism for the communication overhead-reduction is used; this guarantees high levels of performance and scalability. To demonstrate the efficiency of LUNES, we test the simulator with gossip protocols executed on top of networks (representing peer-to-peer overlays), generated with different topologies. Results demonstrate the effectiveness of the proposed approach.