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

Abstract

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.