Molecular dynamics simulations 2015

Molecular dynamics simulations 2015


These course notes are compiled, based on previous course materials, for the Moscow Engineering Physics Institute (MePhi) in Dec 2015, but may be used freely by anybody interested.

Aim: The aim of the course materials is to provide a practical introduction into modern molecular dynamics simulations methods used in materials physics.

Prerequisites: Knowledge of the basics of programming and the Unix environment, the structure of matter and thermodynamics. The course is also suited to chemists.

Contents: Visualization and animation of atomic data. Molecular dynamics simulations, which enable following the motion of a set of pointlike objects (typically but not necessarily atoms). During the course, the students get to write in a guided manner their own molecular dynamics code, capable of simulating atom motion in simple metals. Genetic algorithm and conjugate gradient energy minimization of atomic systems. Overview of quantum mechanical and classical models of atomic interaction, and a detailed description of modern classical force models for metals, semiconductors, ionic and organic materials.

Responsible persons: Prof. Kai Nordlund and Doc. Flyura Djurabekova

Literature: lecture notes. For background material I recommend the books:

  • Allen, Tildesley: "Computer simulation of Liquids" (Oxford University Press, Oxford, England, 1989); still a must-read for a molecular dynamics specialist.
  • D. Frenkel, B. Smit: Understanding Molecular Simulation: From Algorithms to Applications, 2nd edition (Academic Press, 2001)
  • A. R. Leach: Molecular modelling: Principles and applications, 2nd edition (Prentice Hall, 2001)

    Related materials: Short tutorial notes and animations on molecular dynamics and irradiation effects

  • Lecture notes

  • Chapter 1: Introduction, contents and visualization methods
  • Chapter 2: Basics of MD, initialization, time step choice, speedup methods
  • Chapter 3: Neighbour lists, cellular method; introduction to tutorial mdmorse code
  • Chapter 4: Solving the equations of motion
  • Chapter 5: Force calculation, pair potentials, potential fitting
  • Chapter 6: Theory, ensembles, P and T control
  • Chapter 7: Quantum mechanical interaction models
  • Chapter 8: Interaction models for metals
  • Chapter 9: Interatomic potentials for semiconductors
  • Chapter 10: Molecular interaction models
  • Chapter 11: Ionic interactions
  • Chapter 12: Conjugate gradients, genetic algorithms
  • Chapter 13: Repetition


  • 1: Lattice generation, visualization
  • 2: HCP lattice, Gaussian random numbers
  • 3: mdmorse init, neighbourlist
  • 4: Solution of equations of motion
  • 5: Force calculation
  • 6: Cutoff effects, energy conservation
  • 7: Maxwell-Boltzmann distribution, T control
  • 8: Pressure control, thermal expansion
  • 9: Bulk modulus
  • 10: Surface and defect energies
  • 11: Melting temperature by interface method
  • 12: Sintering of nanoclusters, SW potential
  • All lectures and exercises in a single portrait format document (suitable for printing).

    mdmorse code

    Code is provided here without the physically meaningful subroutine contents, since the aim is to write these in the exercises

  • Link to code materials

    dpc code

    The command-line quick atom visualization package dpc is provided here as a .tar.gz package. For installing advice, read "README.INSTALL" after unpacking the code. The (only) documentation is obtained by running dpc without any options.

  • dpc tar.gz package
    Kai Nordlund