Modeling the dynamics of complex molecular systems is difficult since physically relevant distance and time scales are often very long. Consequently, a variety of different coarse-grained molecular dynamics methods, which attempt to bridge gap between short and long scales, has been developed. The talk will focus one such method, multiparticle colision dynamics, for the computation of the mesoscopic dynamics of molecular systems. In particular, polymer and biopolymer dynamics in crowded molecular environments, such as those encountered in the interior of the cell, and the motion of self-propelled nanoparticles in solution will be considered. The mesoscopic simulations were carried out by combining a molecular dynamics description of the molecular with a coarse grained description of the solvent using multiparticle collision dynamics.