Hydrodynamic forces

I am using Autopipe advanced to model a subsea piping system.  There is a vertical pipe going from the surface to the seabed,  but this section is inside a caisson,  meaning it is sheltered from waves and current. Near the seabed,  the piping penetrates the caisson,  and becomes exposed to hydrodynamic effects.  Is there any way to assign waves and current only to parts of the piping and not to the entire model?