In this paper, we consider a system consisting of multiple floating robotic modules performing self-assembly. Faithfully modeling such a system and its inter-module interactions typically involves capturing the hydrodynamic forces acting on the modules using computationally expensive fluid dynamic modeling tools. This poses restrictions on the usability of the resulting models. Here, we present a new approach towards modeling such systems. First, we show how the hardware and firmware of the robotic modules can be faithfully modeled in a high-fidelity robotic simulator. Second, we develop a physics plugin to recreate the hydrodynamic forces acting on the modules and propose a trajectory-based method for calibrating the plugin model parameters. Our calibration method employs a Particle Swarm Optimization (PSO) algorithm, and consists of minimizing the difference between Mean Squared Displacement (MSD) data extracted from real and simulated trajectories of multiple robotic modules.