Time-domain analysis is important for the development of performance-based criteria for the intact stability of ship (level 3 criteria in the 2nd Generation Intact Stability Criteria). It can be implemented to assess directly the vulnerability of ships against various modes of intact stability failure and ensure a sufficient level of safety. In this context, ELIGMOS, a novel time domain simulation code combining a maneuvering model and a seakeeping model, is under development. As the maneuvering model has been the subject of previous paper, the seakeeping part is presented herein and validated in terms of linear and nonlinear vertical motions in head seas. Heave and pitch motions are augmented near the resonant periods, testing the ability of the numerical tool to capture accurately the ship's behaviour, as it plays a dominant role for her direct stability assessment afterwards. Surge motion is considered uncoupled and it is excluded from the system of equations, keeping the forward speed constant. Comparison regarding the seakeeping performance of KVLCC2 is presented against experimental results and results obtained by a 3D-potential flow, frequency domain software as well. Ship's geometry is modelled by means of quadrilateral panels whilst radiation forces were incorporated by means of memory functions by adopting the well-known concept of convolution integrals. The ability of ELIGMOS to capture the effect of geometrical nonlinearities on the vertical motions is demonstrated through preliminary simulation of large amplitude motions of a C11-class containership.