Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solvingNewton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanics force fields. The method is applied mostly in chemical physics, materials science, and biophysics.
Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systemsanalytically; MD simulation circumvents this problem by using numericalmethods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in numerical integration that can be minimized with proper selection of algorithms and parameters, but not eliminated entirely.
For systems that obey the ergodic hypothesis, the evolution of one molecular dynamics simulation may be used to determine macroscopic thermodynamic properties of the system: the time averages of an ergodic system correspond to microcanonical ensemble averages. MD has also been termed "statistical mechanics by numbers" and "Laplace's vision of Newtonian mechanics" of predicting the future by animating nature's forces[1] and allowing insight into molecular motion on an atomic scale.
See also[edit]
Molecular modeling
Computational chemistry
Force field (chemistry)
Comparison of force field implementations
Monte Carlo method
Molecular design software
Molecular mechanics
Multiscale Green's function
Car–Parrinello method
Comparison of software for molecular mechanics modeling
Quantum chemistry
Discrete element method
Comparison of nucleic acid simulation software
Molecule editor
Mixed quantum-classical dynamics
https://en.wikipedia.org/wiki/Molecular_dynamics
Anton is a massively parallel supercomputer designed and built by D. E. Shaw Research in New York, first running in 2008. It is a special-purpose system for molecular dynamics (MD) simulations of proteins and other biological macromolecules. An Anton machine consists of a substantial number of application-specific integrated circuits (ASICs), interconnected by a specialized high-speed, three-dimensional torus network.[1]
Unlike earlier special-purpose systems for MD simulations, such as MDGRAPE-3developed by RIKEN in Japan, Anton runs its computations entirely on specialized ASICs, instead of dividing the computation between specialized ASICs and general-purpose host processors.
https://en.wikipedia.org/wiki/Anton_(computer)
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