HyperLynx SI is optimized for PCB transmission line simulations. In order to simulate something other than this, you need another simulator, or play some tricks. Can you model the fiber connection including transcievers in SPICE? If you can do that, either with another tool, or with a good guess, then you can use that SPICE model in LineSim GHz. Another option might be to use BoardSim to export an accurate model of your PCB traces, and use that model as part of the complete simulation in another tool, such as SystemVision.