A system and method for controlling operation of cylinder with at least an intake and exhaust valve and a piston are described. In one aspect, the method comprises maintaining at least one of the intake and exhaust valves in a closed position during a period. Further, closing the other of the intake and exhaust valves with the piston at a first position from, and then opening the other of the intake and exhaust valves at a second position of the piston closer to bottom center than said first position, during said period.