It is argued that multimedia technology affords an opportunity to better visualise complex relationships often seen in chemistry. This paper describes the influence of chemistry simulation design facets on user progress through a simulation. Three versions of an acid-base titration simulation were randomly allocated to 36 volunteers to examine their interactions with the simulation. The impact of design alterations on the total number of interactions and their patterns was analysed for the following factors: (a) the place of a feature on the screen; (b) alignment of the sequence of instructions; (c) additional instruction before the simulation; and (d) interactivity of a feature. Additionally, interactions between individual factors, such as age, prior experience with science simulations and computer games, perception of the difficulty of science simulations, and general subject knowledge, on one hand, and the efficiency of using the simulation, on the other hand, were examined. The findings suggest that: (a) centrality of the position of an element significantly affects the number of interactions with the element; (b) re-arranging the sequence of instructions on the screen in left-to-right order improves the following of instructions; (c) providing users with additional written advice to follow numbered instructions does not have a significant impact on student behaviour; and (d) interactivity of a feature was found to have a strong positive correlation with the number of interactions with that feature, which warrants a caution about unnecessary interactivity that may hinder simulation efficiency. Surprisingly, neither prior knowledge of chemistry nor the age of the participants had a significant effect on either the number of interactions or the ability to follow on-screen instructions.