The generation of nonlinear waves in a numerical wave using first-order wavemaker theory is discussed comparing numerical results with free Surface data from large scale physical tests (CIEM wave flume) and Stokes wave theories. A general formulation for the analysis of fluid-structure interaction problems is employed to simulate the numerical wave flume using the Particle Finite Element (PFEM). This method uses a Lagrangian description to model the motion of particles in both the fluid and the structure domains. With this work we can conclude that PFEM formulation simulate the generation of natyrally-occurring nonlinear waves with different types for varied wave conditions and at different scales. Like in physical flumes if we use first-order wavemaker theory in numerical flumes unwanted nonlinearities can be found for some wave conditions.