Computer simulations, one of the most powerful tools of science, have many uses. This paper concentrates on the benefits to the social science researcher. Based on our, somewhat paradoxical experiences we had when working with computer simulations, we argue that the main benefit for the researchers who work with computer simulations is to develop a mental model of the abstract process they are simulating. The development of a mental model results in a deeper understating of the process and in the capacity to predict both the behavior of the system and its reaction to changes of control parameters and interventions. By internalizing computer simulations as a mental model, however, the researcher also internalizes the limitations of the simulation. Limitations of the computer simulation may translate into unconscious constrains in thinking when using the mental model. This perspective offers new recommendations for the development of computer simulations and highlights the importance of visualization. The recommendations are different from the recommendations for developing efficient and fast running simulations; for example, to visualize the dynamics of the process it may be better for the program to run slowly.