Naphthalene Energy Minimization

This video illustrates the simple case of minimizing forces in naphthalene to determine its ideal shape. For the sake of the example, all of its atoms were placed at the same location (an impossibly high-energy state), and then allowed settle into positions where the molecule's total energy has been reduced as much as possible. This minimization was performed via an algorithm developed internally at Collective Scientific; the movie was rendered using PyMOL.