The free piston linear engine has the potential to achieve high efficiency and might serve as a viable platform for robust implementation of low temperature combustion schemes (such as homogeneous charge compression ignition - HCCI) due to its ability to vary compression and stroke in response to cylinder and load events. A major challenge is control of the translator motion. Lack of geometric constraint on the piston leads to uncertainty about its top dead center position and timing. While combustion control depends on knowledge of the piston motion, the combustion event also affects the motion profile of the piston. To advance understanding of this coupled system, a numeric model was developed to simulate multiple cycles of a dual cylinder, spring assisted, 2-stroke HCCI, free piston linear engine generator. The MATLAB®/Simulink model depends on simplifications (for scavenging, springs, and alternator), differential relationships (for cylinder pressure and translator dynamics), and empirical relationships (for friction, heat transfer, and combustion). To address the complexity of HCCI combustion within a multi-cycle simulation, an auto-ignition integral, a heat release profile, a heat loss model, and assumptions for combustion duration and efficiency are needed. In this investigation, two knock integral methods are examined along with a Wiebe heat release function. Finally, the effect of total heat release and total heat transfer on translator dynamics are demonstrated. Aside from contributing to the overall energy balance, combustion timing advanced ahead of TDC is shown to allow for adverse work. Increasing the heat transfer, along with advanced combustion timing, leads to increased adverse work and consequentially lower overall efficiency.