A free, hands-on course

Molecular dynamics, from scratch.

A free, hands-on course: learn molecular dynamics from scratch with school maths, live simulations, hand-checked labs, and LAMMPS running in your browser.

Lessons

01

Basics

What MD is, and the smallest loop that makes atoms move.

  1. 1.1What is molecular dynamics?
  2. 1.2Atoms and forces: the Lennard-Jones potential
  3. 1.3Newton's law in code
  4. 1.4The time step
  5. 1.5Euler vs velocity Verlet
  6. 1.6Energy conservation: checking your simulation
  7. 1.7Lab: two atoms by hand
  8. 1.8Lab: integrator extras (shadow energy, precision, RESPA)
02

Building a system

Units, starting structures and the periodic box.

  1. 2.1Units in MD
  2. 2.2Starting positions: lattices
  3. 2.3Starting velocities: Maxwell–Boltzmann
  4. 2.4Periodic boundary conditions
  5. 2.5Cutoffs and the minimum image
  6. 2.6Neighbour lists
  7. 2.7Lab: building a system by hand
  8. 2.8Lab: packing and equilibrating a liquid
03

Ensembles and temperature

Controlling temperature and pressure.

  1. 3.1What temperature means in MD
  2. 3.2NVE, NVT and NPT
  3. 3.3The Berendsen thermostat
  4. 3.4Nosé–Hoover thermostats
  5. 3.5Langevin dynamics
  6. 3.6Pressure and barostats
  7. 3.7Lab: thermostats by hand
  8. 3.8Lab: barostats by hand
  9. 3.9Lab: Monte Carlo vs MD by hand
04

Molecules

Bonds, angles and force fields.

  1. 4.1Bonds and angles
  2. 4.2Dihedrals
  3. 4.3What is a force field?
  4. 4.4Constraints and SHAKE
  5. 4.5Water models
  6. 4.6Lab: a molecule by hand
05

Electrostatics

Long-range charges in a periodic world.

  1. 5.1Coulomb's law in a periodic box
  2. 5.2Ewald summation
  3. 5.3Particle-mesh Ewald
  4. 5.4Polarizable models
  5. 5.5Lab: electrostatics by hand
06

Analysis

Turning trajectories into numbers you can compare with experiment.

  1. 6.1Radial distribution function
  2. 6.2Mean squared displacement and diffusion
  3. 6.3Velocity autocorrelation
  4. 6.4Van Hove functions
  5. 6.5Ionic conductivity
  6. 6.6Onsager coefficients and transference numbers
  7. 6.7Lab: analysis by hand
  8. 6.8Lab: error bars by hand
  9. 6.9Lab: finite-size effects by hand
  10. 6.10Lab: viscosity by hand
  11. 6.11Lab: lifetimes by hand
  12. 6.12Lab: structure factor by hand
  13. 6.13Lab: dielectric constant and rotation by hand
07

Beyond

From your own code to research tools.

  1. 7.1From toy code to LAMMPS and GROMACS
  2. 7.2Machine-learning potentials
  3. 7.3Enhanced sampling: metadynamics
  4. 7.4Lab: beyond, by hand
  5. 7.5Lab: free energies by hand