Wave run-up is the vertical water uprush that occurs when an incident wave impacts on a surface-piercing body. This phenomenon is particularly relevant when waves of high steepness interact with large structures as a result of significant nonlinear interactions between incident and diffracted wave fields. The extent can be further amplificated in the presence of appreciable motions of the structure as radiated waves take part in the network of wave-wave interactions. Underprediction of the run-up height exposes ships and offshore platforms to severe localised structural damages. A sufficient deck elevation proves to be mostly effective in overcoming these issues. Over the last decades, sustained research has been produced on wave run-up by fixed structures. However, a complete understanding of the effects of wave radiation by moving structures on the run-up flow is still far from being achieved. In the wake of a recent publication dealing with the presence of the surge motion, this graduation project aims to take a further step forward in the research by evaluating the wave run-up amplification due to heave. With this purpose, a validated numerical wave tank is established in ComFLOW and the case study of a two-dimensional rectangular structure is addressed. As a side objective, a piston-type wavemaker based on second-order wave generation theory is first implemented in ComFLOW. The performance of the wave board wave generation method is thoroughly discussed with regard to accuracy, propagation stability, numerical dissipation and dispersion in the context of nonlinear regular waves.