Molecular dynamics

Molecular dynamics is a deterministic technique, proposed by Alder and Wainwright in 1959 , used to create trajectories for atoms and molecules.

• Ab initio molecular dynamics
• Barostats
• Beeman's algorithm
• Blue-moon ensemble
• Car-Parrinello technique
• Charge equilibration
• Constant chemical potential molecular dynamics (CμMD)
• Constraints
• Event-driven molecular dynamics
• Flying ice cube
• GWTS algorithm
• Heat exchange algorithm
• Initial configuration
• Integrators for molecular dynamics
• Liouville-von Neumann molecular dynamics
• Mass-stat
• Materials modelling and computer simulation codes
• Milestoning
• Multi-particle collision dynamics
• Multi-scale shock technique
• Non-equilibrium molecular dynamics (NEMD)
• Polarizable point dipoles
• Rigid bodies
• Thermostats
• Time step
  • RESPA a multiple time step method.
• Velocity Verlet algorithm
• Verlet leap-frog algorithm
• Virial pressure

General reading

• M. P. Allen and D. J. Tildesley "Computer Simulation of Liquids", Oxford University Press (1989) Chapter 3.
• J. M. Haile "Molecular Dynamics Simulation: Elementary Methods", John Wiley & Sons, Inc. (1997) ISBN 978-0-471-18439-3
• Daan Frenkel and Berend Smit "Understanding Molecular Simulation: From Algorithms to Applications", Second Edition (2002) ISBN 0-12-267351-4 Chapter 4.
• D. C. Rapaport "The Art of Molecular Dynamics Simulation", 2nd Edition, Cambridge University Press (2004)
• Michael P. Allen "Introduction to Molecular Dynamics Simulation", in Computational Soft Matter: From Synthetic Polymers to Proteins, NIC Series Volume 23 (2004)