A Hands-On Introduction to Molecular Dynamics

We present an introduction to the chemical and computational aspects of the molecular dynamics (MD) simulation technique. Using just a few elementary ideas from classical mechanics and numerical analysis, and linear chains of identical particles as example systems, we take the reader through the ste...

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Bibliographic Details
Published in:Journal of chemical education 2002-05, Vol.79 (5), p.601
Main Authors: Lamberti, Vincent E, Fosdick, Lloyd D, Jessup, Elizabeth R, Schauble, Carolyn J. C
Format: Article
Language:English
Subjects:
Chemistry
Classical mechanics
Computer simulation
Lesson plans
Molecular dynamics
Molecules
Numerical analysis
Organic chemistry
Science education
Simulation
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Summary:We present an introduction to the chemical and computational aspects of the molecular dynamics (MD) simulation technique. Using just a few elementary ideas from classical mechanics and numerical analysis, and linear chains of identical particles as example systems, we take the reader through the steps required for the design and analysis of a simple molecular dynamics experiment. We employ the Hooke's law model for the interactions between the particles since its visualization in terms of masses and springs provides a natural model for chemical bonds. We derive the classical equations of motion in detail for the three-particle chain. We then introduce two simple methods for numerically integrating the equations of motion, one based on Euler's method for differential equations, and the other a more accurate algorithm developed by Verlet. We analyze the dynamics of the three-particle system in terms of its normal modes of vibration. Finally, exploiting the closed-form solution admitted by the Hooke's law potential, we compare the errors generated by the two integration algorithms. As supplemental material, we provide a basic MD implementation using the Euler algorithm in both Fortran and C and a set of suggested exercises.
ISSN:0021-9584
1938-1328
DOI:10.1021/ed079p601