A method of controlling an internal combustion engine and system including the engine is provided. The method may include closing an exhaust valve of a combustion chamber of said engine during a cylinder cycle prior to opening an intake valve of said combustion chamber. The method may include, when a desired engine torque is a predetermined torque or greater, supplying a first pilot fuel into said combustion chamber after said exhaust valve closing and supplying a first main fuel into said combustion chamber after the combustion of said first preliminary fuel during the cylinder cycle. The method may include, when a desired engine torque is less than said predetermined torque, supplying a second pilot fuel into said combustion chamber after said exhaust valve closing during the cylinder cycle and supplying a second main fuel into said combustion chamber after the supplying of said second pilot fuel into said combustion chamber.