An empirical survey explores the effectiveness of using molecular modeling software in upper division physical chemistry at the University of North Dakota. All of the students taking the course are senior or graduate level students in chemistry. Based on the feedback from the survey, coursework in the future semesters is to be improved and redesigned. Students completed a survey questionnaire about which they express what they think of the course. A pretest survey is also performed to determine the students’ knowledge of the UNIX operating system and user interface (Unix Terminal). All but one student had no prior programming or UNIX environment experience. Students were given a series of tutorials, which provided detailed instructions on the UNIX user interface (terminal) and the software packages. Within the UNIX environment, students learned how to perform protein minimizations, run and analyze molecular dynamics (MD) simulations, and to solve the linearized Poisson-Boltzmann equation to simulate protein titrations. Students learn to use VMD, NAMD and MacroDox. Another post-test survey analyzed the student views after the end of the course session.  From the results obtained, students indicate they would find it helpful if they were taught how to use the UNIX terminal window and the vi editor in particular before the beginning of the modeling exercises. Learning UNIX first will allow students to better find, open, close, save and edit input and output files and also on how to perform tasks like remote machine login and usage. This will be implemented in the future offerings of the course.

Teaching UNIX based molecular modeling in upper division undergraduate chemistry

251st National Meeting (2016)

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