We model regular and irregular design waves of interest in coastal and ocean engineering, using a Numerical Wave Flume (NWF) based on a Moving Particle Semi-Implicit (MPS) method. A key feature of the model is the implementation of a new scheme for the artificial viscosity, which is original to the Smoothed Particle Hydrodynamics (SPH) method and is here formalised into the MPS context. In addition, we complement the NWF with a wave generator based on the dynamic boundary method approach, and a wave absorption mechanism using a numerical damping zone. We show that accurately calibrating the new terms has a strong effect in preventing particle clustering and tensile instability, and allows a precise simulation of wave phenomena of interest in ocean and coastal engineering. The NWF-MPS model is validated using the available analytical and experimental benchmarks, and is then applied to reproduce a violent wave impact on a vertical wall breakwater. Interestingly, the novel NWF-MPS requires a much lower number of particles to obtain a similar level of accuracy as compared to analogous SPH simulations run on similar machines.