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7745787 
Journal Article 
A Simple Molecular Dynamics Lab To Calculate Viscosity as a Function of Temperature 
Eckler, LH; Nee, MJ 
2016 
Yes 
Journal of Chemical Education
ISSN: 0021-9584 
American Chemical Society 
93 
5 
927-931 
English 
WOS:000376333100023 
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. © 2016 The American Chemical Society and Division of Chemical Education, Inc. 
Upper-Division Undergraduate; Physical Chemistry; Laboratory Instruction; Computer-Based Learning; Alkanes/Cycloalkanes; Molecular Mechanics/Dynamics; Transport Properties