Molecular dynamics

• Initial configuration
• Verlet leap-frog algorithm
• Velocity Verlet algorithm
• Time step
  • RESPA, a multiple time step method
• Thermostats
• Barostats
• Virial pressure
• LINCS
• RATTLE
• SETTLE
• SHAKE
  • M-SHAKE
  • P-SHAKE
  • RD-SHAKE
  • Q-SHAKE
• WIGGLE
• Rigid bodies
• Event-driven molecular dynamics
• Ab initio molecular dynamics

General reading

• D. C. Rapaport "The Art of Molecular Dynamics Simulation", Cambridge University Press