Surface roughness induced influence to the contact angle are orders of magnitudes larger in surface dimensions, than what you will likely be able to simulate. However, simulating water contact angles is generally possible. We currently do that for carbon contamination on titanium dioxide surfaces. We also have an in-house code to measure the equilibration of the contact angle over a whole trajectory.
I agree to your point (Surface roughness induced influence to the contact angle are orders of magnitudes larger in surface dimensions). But is it possible to simulate the same on mesoscale level by developing any model? Or if I group the molecules to convert into beads, is there any way to do structural simulation which include atomistic interaction?
Yes, you can do that. It might be best to start with all-atom systems, to see what contact angle you already get there. We used surfaces (fully periodic) of about 20-30 nm side length and a water cube of about 6nm side length, hovering above by few angstrom.
We usually had convergent contact angles after about 20ns of simulation time.