Summer Book Club 2014: Molecular Simulations and Theory | Learning | Beckstein Lab

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Summer Book Club 2014: Molecular Simulations and Theory

Summer Book Club 2014: Molecular Simulations and Theory

This summer’s Lab Book Club is designed to provide a thorough review of fundamental concepts for understanding biomolecular simulation and, in particular, molecular dynamics simulations (MD). The material is primarily based on textbook reading1,2 and has been chosen to roughly fit into the 8-9 weeks of the ASU summer calendar; several optional topics placed at the end to permit some flexibility in the coverage of material. All textbooks that are used are available online through ASU. Weekly topics are roughly chosen based on chapters from Statistical Mechanics: Theory and Molecular Simulation by Mark Tuckerman.1

The Book Club is organized by Sean Seyler. Contact him if you are interested in participating.

Reading materials

All reading materials are either available through the Zotero Group Becksteinlab Book Club or as ebooks through ASU1,2.

For additional information you can also have a look the old course pages for PHY494/PHY598/CHM598 — Simulation approaches to Bio- and Nanophysics.


The Syllabus for 2014 is available from the Zotero group. In outline:

Week 1
Classical mechanics and statistical mechanics
Tuckerman ch 1 & 2
Week 2
The microcanonical ensemble and MD
Tuckerman ch 3
Week 3
The canonical ensemble
Tuckerman ch 4
Week 4
Isobaric ensembles
Tuckerman ch 5
Week 5
Free energies: equilibrium approaches
Tuckerman ch 8
Week 6
Free energies: non-equilibrium work methods
Tuckerman ch 8
Week 7
Time-dependent statistical mechanics
Tuckerman ch 13
Week 8
Langevin equations
Tuckerman ch 15
Week 9
Monte Carlo methods
Tuckerman ch 7


  1. a b c Mark E. Tuckerman. Statistical Mechanics: Theory And Molecular Simulation, 2010, Oxford University Press, Oxford (ebook at ASU)
  2. a b Daan Frenkel and Berend Smit. Understanding molecular simulation: from algorithms to applications. 2002, 2nd ed., Computational science series. Academic Press. (eBook at ASU)

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