A method for determining cylinder air charge and/or cylinder burned gas for an internal combustion engine system. The engine system includes cylinders, each one of such cylinders having at least one intake valve and at least one exhaust valve in communication with such cylinder. The method determines one of a plurality of different scenarios, each one of the scenarios representing a geometrical relationship between opening and closing of the intake valve relative to closing of the exhaust valve. The cylinder air charge and/or cylinder burned gas is calculated in accordance with the determined one of the plurality of scenarios. In one embodiment, the engine system stores a plurality of different software modules. The method selects one of the plurality of software modules in accordance with the determined one of the plurality of scenarios. The cylinder air charge and/or cylinder burned gas calculation comprises executing the selected one of the modules. In one embodiment, a memory stores a relationship between volume occupied by residual gas in the at least one cylinders at a predetermined position of the at least one cylinder in the engine during the cycle determined in accordance with each one of the plurality of scenarios for each of a plurality of different intake valve opening and exhaust valve closing conditions. The method includes: determining from the memory the volume occupied by residual gas in the at least one cylinders at a predetermined position of the at least one cylinder in the engine during the cycle for the intake valve opening and exhaust valve closing conditions; and, determining from volume occupied by residual gas in the at least one cylinders at a predetermined position of the at least one cylinder in the engine during the cycle the cylinder air charge and/or cylinder burned gas.