Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules, and is thus a type of N-body simulation. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamical evolution of the system.
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- Molecular dynamics is not primarily about making movies of molecules. More often it is about developing quantitative predictions of molecular size and shape, flexibilities, interactions with other molecules, behavior under pressure, and the relative frequency of one state or conformation compared to another. The complex nature of the force fields involved and the large size of typical molecular systems mean that molecular dynamics is almost always chaotic. The changes in a molecule that occur over time are important, but these should be understood in terms of changes in averaged quantities, structural forms, or families of “nearby” structures. Molecular dynamics relies on time-stepping to compute successive snapshots, but these are often used for sampling a probability distribution, or else a number of evolving paths are averaged to describe the likely sequence of changes that would be observed in a typical evolution of the molecule.
- Ben Leimkuhler and Charles Matthews, Molecular Dynamics: With Deterministic and Stochastic Numerical Methods (2015), Ch. 1 : Introduction