The method comprises controlling the fuel injection system and/or the exhaust system to control the cylinder pressure at predetermined frequencies. In particular the method comprises controlling the fuel injection system to initiate fuel injection by gradually increasing the fuel injection rate. The pressure is calculated or measured, and a frequency analysis such as an FFT analysis can be performed to determine the pressure component at each frequency. A mathematical model is used to determine the resulting vibration at each frequency. By proper control of the fuel injection, and in particular the initial phase thereof, a smoother pressure curve with less high-frequency content and/or reduced maximum pressure can be achieved. It is thereby possible to control the frequency content of the cylinder pressure, and predetermined frequencies can be suppressed.