This article contributes to a major research domain in physics education which is focused on the study of the effects of various types of teaching interventions aimed to help students' alternative conceptions transformation. Computer simulations are applications of special interest in physics teaching because they can support powerful modeling environments involving physics concepts and processes. Two groups (control and experimental) of 15-16 years old students were studied to determine the role of computer simulations in the development of functional understanding of the concepts of velocity and acceleration in projectile motions. Both groups received traditional classroom instruction on these topics; the experimental group used computer simulations also. The results presented show that students working with simulations exhibited significantly higher scores in the research tasks. Our findings strongly support the fact that computer simulations may be used as an alternative instructional tool, in order to help students confront their cognitive constraints and develop a functional understanding of physics.