Dear MinJi Jo,
Simulation 1 from the recent FAST workshop (materials available from: FAST, the NREL 5-MW turbine uses a controller implemented as a DLL (i.e., DISCON.dll) that requires FAST’s interface to GH Bladed-style DLLs, which is not a default option in the current version of FAST. I suspect when you are running Simulation 2 in Simulink, that you are enabling turbine control, but not calling the controller DLL because the default FAST S-Function does not have an interface to the GH Bladed-style DLL. This is the reason for the differences you are seeing between the results obtained from the open-loop FAST simulation in Simulink and the results obtained directly from the FAST executable.
The main reason for running FAST from within Simulink is so that controller logic can be implemented in Simulink.
Best regards,