It is common that middle school students have difficulty understanding Newton's laws of motion. Computer simulations are found useful in helping students learn principles of Newtonian motion. The research investigates how middle school students react to a computer program called "ThinkerTools", and how their use of the ThinkerTools package influenced their learning. This study also seeks to identify the problems that student encountered while using the program. Student's homework answers are compared against their pretest answers and classroom observations to realize the process of an individual's conceptual change. Questionnaire answers are processed and presented quantitatively in order to understand student reactions toward using the ThinkerTools program. Students' posttest results against pretest performances are compared quantitatively in order to realize students' gains from using the program. Selected students' conversations are audio taped and a subset of these students were interviewed to examine intensively how they used this software. In general this study found that students' understanding of Newtonian motion and kinematics was improved by the use of the ThinkerTools program. With the help of simulations, accompanying materials, and activities, students' prior knowledge was connected to the physics principles. Moreover, this program was found to promote conceptual change by allowing students to design their own experiments and to observe the results from the computer outcome. The computer activities also promoted interactions between students when they worked in groups and helped students construct their understanding of Newton's laws of motion collaboratively. However, more guidance would be necessary if the activities required more advanced knowledge to understand the concepts behind the simulations. Otherwise, the simulations could possibly lead students to develop alternative conceptions. Overall, students were interested in using the ThinkerTools package and were willing to use it to learn physics concepts in further units.