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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 various branches of the DEM family are the distinct element method proposed by Peter A. Cundall and Otto D. L. Strack in 1979, [5] the generalized discrete element method, [6] the discontinuous deformation analysis (DDA) and the finite-discrete element method concurrently developed by several groups (e.g., Munjiza and Owen).
For example, many simulations have historically used a united-atom representation in which each terminal methyl group or intermediate methylene unit was considered one particle, and large protein systems are commonly simulated using a bead model that assigns two to four particles per amino acid.
VisSim - system simulation and optional C-code generation of electrical, process, control, bio-medical, mechanical and UML State chart systems. Vortex (software) - a complete simulation platform featuring a realtime physics engine for rigid body dynamics, an image generator, desktop tools (Editor and Player) and more. Also available as Vortex ...
In an ab initio MD simulation, the total energy of the system is calculated at each time step using density functional theory (DFT) or another method of quantum chemistry. The forces acting on each atom are then determined from the gradient of the energy with respect to the atomic coordinates, and the equations of motion are solved to predict ...
For a system of particles with masses , with coordinates = that constitute a time-dependent random variable, the resulting Langevin equation is [2] [3] ¨ = ˙ + (), where () is the particle interaction potential; is the gradient operator such that () is the force calculated from the particle interaction potentials; the dot is a time derivative ...
TCAM (Transport Chemical Aerosol Model; TCAM): a mathematical modelling method (computer simulation) designed to model certain aspects of the Earth's atmosphere. TCAM is one of several chemical transport models, all of which are concerned with the movement of chemicals in the atmosphere, and are thus used in the study of air pollution.
Dissipative particle dynamics (DPD) is an off-lattice mesoscopic simulation technique [1] which involves a set of particles moving in continuous space and discrete time. Particles represent whole molecules or fluid regions, rather than single atoms, and atomistic details are not considered relevant to the processes addressed.