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A molecular dynamics simulation requires the definition of a potential function, or a description of the terms by which the particles in the simulation will interact. In chemistry and biology this is usually referred to as a force field and in materials physics as an interatomic potential .
The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (a molecular mechanics approach), or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons (a quantum chemistry ...
Atomistic interactions in crystal systems significantly deviate from those in molecular systems, [13] e.g. of organic molecules. For crystal systems, particularly multi-body interactions, these interactions are important and cannot be neglected if a high accuracy of the force field is the aim.
A classical molecular dynamics computer simulation of a collision cascade in Au induced by a 10 keV Au self-recoil. This is a typical case of a collision cascade in the heat spike regime. Each small sphere illustrates the position of an atom, in a 2-atom-layer-thick cross section of a three-dimensional simulation cell.
All-atomistic molecular mechanics methods have the following properties: Each atom is simulated as one particle; Each particle is assigned a radius (typically the van der Waals radius), polarizability, and a constant net charge (generally derived from quantum calculations and/or experiment)
Atomistic resolution models alone are presently not efficient enough to handle large system sizes and simulation timescales. [1] [2] Coarse graining and fine graining in statistical mechanics addresses the subject of entropy , and thus the second law of thermodynamics.
Force fields are used for the simulation of metals, ceramics, molecules, chemistry, and biological systems, covering the entire periodic table and multiphase materials. Today's performance is among the best for solid-state materials, [ 51 ] [ 52 ] molecular fluids, [ 21 ] and for biomacromolecules, [ 53 ] whereby biomacromolecules were the ...
Constraint algorithms are often applied to molecular dynamics simulations. Although such simulations are sometimes performed using internal coordinates that automatically satisfy the bond-length, bond-angle and torsion-angle constraints, simulations may also be performed using explicit or implicit constraint forces for these three constraints.