Just remember that everything is relative to the current execution path of the makefile. If you have a dependency that is not in the same path, you need to specify the path in the dependency list. Maybe you need this?
Code:
Sim: Energy/Energy.o #...
g++ -o Sim Energy/Energy.o #...
#...
Energy/Energy.o: Energy/Energy.cpp
g++ -c -Wno-deprecated Energy/Energy.cpp -o Energy/Energy.o
ta0kira