A method and system to avoid collision of piston and engine valves is provided. This facilitates use of a fully flexible variable valve actuation system over its operating range, without arbitrary constraints. Included is actuation control of the engine valve, determination of a crank angle at which to initiate engine valve opening, and determination of a desired valve lift, and, duration of valve open time. Opening profile for the engine valve is estimated. A first and a second crank angle are calculated, based upon the estimated opening profile. The crank angle to initiate engine valve opening is determined by adding a safety margin to the second crank angle. The method determines a maximum valve lift, given the duration of valve open time and an engine valve opening crank angle, and a minimum duration of valve open time, given a valve lift and an engine valve opening crank angle.