You can open whatever file you want, no matter its location. Just specify the correct location in the disk. Usually, if a specific location is not specified it looks at the current folder location (where the simulator.cpp is).
Example (sth like this for XP)
If you put
ifstream in("C:\\Windows\\Documents and Settings\\User_Name\\Desktop\\Assembler\\Assembler_Folder\\output.o");
then it most likely look for output.o in the folder that simulator.cpp is.
Note that you need \\ not \