The spontaneous imbibition of liquid in nanopores of different roughness is investigated using coarse grain molecular dynamics (MD) simulation. The numerical model is presented and the simplifying assumptions are discussed in detail. The molecular-kinetic theory introduced by Blake is used to describe the effect of dynamic contact angle on fluid imbibition. The capillary roughness is modeled using a random distribution of coarse grained particles forming the wall. The Lucas-Washburn equation is used as a reference for analyzing the imbibition curves obtained by simulation. Due to the statistical nature of MD processing, a comprehensive approach was made to average and smooth the data to accurately define a contact angle. The results are discussed in terms of effective hydrodynamic and static capillary radii and their difference as a function of roughness and wettability.