Molecular dynamics

Molecular dynamics (MD) is a <a href="/facts/Computer_simulation/Re6o8vzN">computer simulation</a> method for analyzing the <a href="/facts/Motion_(physics)/dCnP7MlB">physical movements</a> of <a href="/facts/Atoms/FoQ4kGN5">atoms</a> and <a href="/facts/Molecules/N9ljSfFq">molecules</a>. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the <a href="/facts/Dynamics_(mechanics)/JLk81H71">dynamic</a> "evolution" of the system. In the most common version, the <a href="/facts/Trajectory/STNN33FK">trajectories</a> of atoms and molecules are determined by <a href="/facts/Numerical_integration/MwJnvcDV">numerically solving</a> <a href="/facts/Newton%2527s_laws_of_motion/XKzGTXK1">Newton's equations of motion</a> for a system of interacting particles, where <a href="/facts/Force_(physics)/LNAUWMwK">forces</a> between the particles and their <a href="/facts/Potential_energy/I03KLbmn">potential energies</a> are often calculated using <a href="/facts/Interatomic_potential/EgJjsSeh">interatomic potentials</a> or <a href="/facts/Molecular_mechanics/6wPpARWP">molecular mechanical</a> <a href="/facts/Force_field_(chemistry)/p9u8nVk8">force fields</a>. The method is applied mostly in <a href="/facts/Chemical_physics/VEqp9VrK">chemical physics</a>, <a href="/facts/Materials_science/N5HrXRYW">materials science</a>, and <a href="/facts/Biophysics/l9u5gqCy">biophysics</a>.
Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such <a href="/facts/Complex_systems/eGG3B1nn">complex systems</a> analytically; MD simulation circumvents this problem by using <a href="/facts/Numerical_analysis/QT9cYa9z">numerical</a> methods. However, long MD simulations are mathematically <a href="/facts/Condition_number/9Tjtk6wh">ill-conditioned</a>, generating cumulative errors in numerical integration that can be minimized with proper selection of algorithms and parameters, but not eliminated.
For systems that obey the <a href="/facts/Ergodic_hypothesis/uHwY6qH9">ergodic hypothesis</a>, the evolution of one molecular dynamics simulation may be used to determine the macroscopic <a href="/facts/Thermodynamic/q4hIx3yP">thermodynamic</a> properties of the system: the time averages of an ergodic system correspond to <a href="/facts/Microcanonical_ensemble/L4fE6SxT">microcanonical ensemble</a> averages. MD has also been termed "<a href="/facts/Statistical_mechanics/6zMsNYYG">statistical mechanics</a> by numbers" and "<a href="/facts/Laplace/6ktp0txb">Laplace</a>'s vision of <a href="/facts/Newtonian_mechanics/XKzGTXK1">Newtonian mechanics</a>" of predicting the future by animating nature's forces and allowing insight into molecular motion on an atomic scale.

Molecular dynamics open-in-new

Molecular dynamics