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In this paper, we present a quantitative, trajectory-based method for calibrating stochastic motion models of water-floating robots. Our calibration method is based on the Correlated Random Walk (CRW) model, and consists in minimizing the Kolmogorov-Smirnov (KS) distance between the step length and step angle distributions of real and simulated trajectories generated by the robots. First, we validate this method by calibrating a physics-based motion model of a single 3-cm-sized robot floating at a water/air interface under fluidic agitation. Second, we extend the focus of our work to multi-robot systems by performing a sensitivity analysis of our stochastic motion model in the context of Self-Assembly (SA). In particular, we compare in simulation the effect of perturbing the calibrated parameters on the predicted distributions of self-assembled structures. More generally, we show that the SA of water-floating robots is very sensitive to even small variations of the underlying physical parameters, thus requiring real-time tracking of its dynamics.