A method and system is provided of controlling a pump having a pumping element comprising: determining, by a controller, a suspension of one or more fuel delivery events for a pumping element of the at least one pumping element; subsequent to determining the suspension of the one or more fuel delivery events, providing, by the controller, a first command to open an inlet valve of the pumping element to remove a portion of residual fluid within a pumping chamber based on pressure within the pumping chamber of the pumping element; and subsequent to providing the first command, providing, by the controller, a second command to close the inlet valve of the pumping element based on a top dead center (TDC) position of the pumping element.