A Simple Molecular Dynamics Lab To Calculate Viscosity as a Function of Temperature

A simple molecular dynamics experiment is described to demonstrate transport properties for the undergraduate physical chemistry laboratory. The AMBER package is used to monitor self diffusion in n-hexane. Scripts (available in the Supporting Information) make the process considerably easier for students, allowing them to focus on the simulations and their meaning. Mean squared displacements are determined as a function of simulation time for 250 ps in a small simulation box at a variety of temperatures. From these, the Einstein-Smoluchowski and Stokes-Einstein relationships are used to determine the viscosity, which can be directly compared to literature values. The needed trajectories can be calculated in less than 1 h and analyzed in a second hour, leaving a third hour for further explorations as appropriate.