Computer simulations combined with games have been successfully used to teach conceptual physics. However, there is no clear methodology for guiding the design of these types of games. To remedy this, we propose a structured methodology for the design of conceptual physics games that explicitly integrates the principles of the intrinsic integration approach for designing instructional games (Habgood & Ainsworth, 2011) with an atomic analysis of the structure of games (Cook, 2007; Cousins, 2005; Koster, 2005). To test this approach, we redesigned an existing game to teach electrostatics and compared the educational effectiveness of the original and redesigned versions. Our studies also compared an endogenous fantasy version of the game with a non-fantasy version. Our results showed that students who played the game which had been redesigned using the Atomic Intrinsic Integration Approach achieved a statistically significant improvement in results and showed fewer conceptual problems than the students who played the original version. The fantasy and non-fantasy versions, however, did not display any significant differences in outcomes. Based on the analysis and redesign of the game, we defined one possible methodology to assist in the design of games for the conceptual understanding of physics. (Contains 3 tables and 8 figures.)