Lundquist, Karl; Herndon, Conner; Harty, Tyson H.; Gumbart, James C.
Accelerating the use of molecular modeling in the high school classroom with VMD Lite

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 approximate to 70 students with overall positive reception. Remaining deficiencies in conceptual understanding were noted, however, and the module has been revised in response. (c) 2016 by The International Union of Biochemistry and Molecular Biology, 44:124-129, 2016.


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