Computer-aided simulations are routinely used to predict a prototype's performance. High-fidelity physics-based simulators might be computationally expensive for design and optimization, spurring the development of cheap deep-learning surrogates. The resulting surrogates often struggle to generalize and predict novel scenarios beyond their training domain. We propose a two-stage methodology addressing the challenge of generalization. It employs physics-based simulators, supplemented with ordinary differential equations integrated into the recurrent architecture, to learn the intrinsic dynamics. The proposed approach captures the inherent causality and generalizes the dynamics irrespective of a data source. The presented numerical experiments encompass five fundamental structural engineering scenarios, including beams on Winkler foundations based on Euler-Bernoulli and Timoshenko theories, beams under moving loads, and catenary-pantograph interactions in railways. The proposed methodology outperforms conventional recurrent methods and remains invariant to data sources, showcasing its efficacy. Numerical experiments highlight its prospects for design optimization, predictive maintenance, and enhancing safety measures.