A system includes an internal combustion engine having a number of cylinders, with at least one of the cylinders plumbed to have a complete recycle of the exhaust gases from the cylinder. The system further includes the completely recycled cylinder having an EGR stroke cycle, and the non-recycled cylinders of the engine having an exhaust stroke cycle. The system includes the EGR stroke cycle being distinct from the exhaust stroke cycle. An amount and composition of the exhaust gases from the recycled cylinder are distinct from the amount and composition of the exhaust gases from the non-recycled cylinders, at least at certain operating conditions of the engine.