Molecular Dynamics Simulations

Molecular Dynamics can be defined as a computer simulation technique that permits the prediction of time evolution of an interacting particular system involving the generation of atomic trajectories of a system using numerical integration of Newton’s equation of motion for a specific interatomic potential defined by an initial condition and boundary condition. Particularly important application of MD simulation is to determine how a biomolecular system will respond to some perturbation. In each of these cases, one should generally perform several simulations of both the perturbed and unperturbed systems in order to identify consistent differences in the results. MD simulations are used to describe the atomic and molecular properties of protein, drug-target interactions, solvation of compounds, and conformational changes that a protein or compound may undergo under various conditions. Molecular simulation methods can basically be separated into quantum mechanics (QM) methods, which treat electrons as the fundamental interactive particles of the system, and classical mechanics (CM) methods, which treat individual atoms or groups of atoms as the fundamental interactive particles of the system. Molecular simulation methods can basically be separated into quantum mechanics (QM) methods, which treat electrons as the fundamental interactive particles of the system, and classical mechanics (CM) methods, which treat individual atoms or groups of atoms as the fundamental interactive particles of the system.

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