A metrology system can be integrated within a lithographic apparatus to provide integrated metrology within the lithographic process. However, this integration can result in a throughput or productivity impact of the whole lithographic apparatus which can be difficult to predict. It is therefore proposed to acquire throughput information associated with a throughput of a plurality of substrates within a lithographic apparatus, the throughput information including a throughput parameter, and predict, using a throughput simulator, a throughput using the throughput parameter as an input parameter. The throughput simulator may be calibrated using the acquired throughput information. The impact of at least one change of a throughput parameter on the throughput of the lithographic apparatus may be predicted using the throughput simulator.