MSE 597G An Introduction to Molecular Dynamics

By Alejandro Strachan

Purdue University



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Molecular dynamics (MD) simulations are playing an increasingly important role in many areas of science and engineering, from biology and pharmacy to nanoelectronics and structural materials. Recent breakthroughs in methodologies and in the development of first principles-based interatomic potentials significantly increased the range of applicability of MD and the accuracy of its predictions even for new materials not yet fabricated or synthesized. Such predictive power indicates that MD has the potential to play a key role in guiding the design and optimization of new materials with improved properties tailored for specific applications.

The goal of this short course is to provide an introduction to the theory and algorithms behind MD simulations, describe some of the most exciting recent developments in the field and exemplify with a few applications applications. The series also includes a tutorial on the nano-Materials Simulation Toolkit, an online MD simulation tool available at the nanoHUB. This provides users with a hands-on experience with MD simulations and enables further exploration of some of the concepts described in the lectures.

These lectures were taught at Purdue University during the Fall semester of 2008 as part of MSE597G “Modeling and Simulation of Materials”.

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Researchers should cite this work as follows:

  • Alejandro Strachan (2008), "MSE 597G An Introduction to Molecular Dynamics,"

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Lecture Number/Topic Online Lecture Video Lecture Notes Supplemental Material Suggested Exercises
MSE 597G: An Introduction to Molecular Dynamics View Flash View Notes (pdf)
MSE 597G Lecture 1: Classical Mechanics View Flash View Notes (pdf)
MSE 597G Lecture 2: Statistical Mechanics I View Flash View Notes (pdf)
Basic physics: statistical mechanics.

MSE 597G Lecture 3: Statistical Mechanics II View Flash View Notes (pdf)
Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.

Running MD on the nanoHUB: The nano-MATERIALS Simulation Toolkit View
A quick demostration of the nanoHUB tool: nano-Materials Simulation Toolkit.

MSE 597G Lecture 4: Interatomic potentials I View Flash View Notes (pdf)
Interatomic potentials: pairwise potentials.

MSE 597G Lecture 5: Interatomic potentials II View Flash View Notes (pdf)
Embedded atom model for metals, Three body terms for semiconductors: Stillinger-Weber, Electrostatics and Covalent interactions.

MSE 597G Lecture 6: Interatomic potentials III View Flash View Notes (pdf)
Reactive force fields, Parameterization of interatomic potentials

MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations View Flash View Notes (pdf)
Thermostats and barostats, Linear methods for energy and force calculations, Coarse graining or mesodynamics, Validation and Verification.