title: Accelerating the use of molecular modeling in the high school classroom with VMD Lite.
abstract: It is often difficult for students to develop an intuition about molecular processes, which occur in a realm far different from day-to-day life. For example, thermal fluctuations take on hurricane-like proportions at the molecular scale. Students need a way to visualize realistic depictions of molecular processes to appreciate them. To this end, we have developed a simplified graphical interface to the widely used molecular visualization and analysis tool Visual Molecular Dynamics (VMD) called VMD lite. We demonstrate the use of VMD lite through a module on diffusion and the hydrophobic effect as they relate to membrane formation. Trajectories from molecular dynamics simulations, which students can interact with freely, illustrate the dynamical behavior of lipid molecules and water. VMD lite was tested by ∼70 students with overall positive reception. Remaining deficiencies in conceptual understanding were noted, however, and the module has been revised in response.
authors.affiliation: School of Physics, Georgia Institute of Technology, Atlanta, Georgia, 30332.
authors.forename: Karl
authors.initials: K
authors.lastname: Lundquist
authors.affiliation: School of Physics, Georgia Institute of Technology, Atlanta, Georgia, 30332.
authors.forename: Conner
authors.initials: C
authors.lastname: Herndon
authors.affiliation: Jasper County High School, Monticello, Georgia, 31064.
authors.forename: Tyson H
authors.initials: TH
authors.lastname: Harty
authors.affiliation: School of Physics, Georgia Institute of Technology, Atlanta, Georgia, 30332.
authors.forename: James C
authors.initials: JC
authors.lastname: Gumbart
mesh_terms: D056004:Molecular Dynamics Simulation; D012574:Schools; D012984:Software; D013663:Teaching
keywords: MD simulations; active learning; molecular visualization; student misconceptions