Drude particles are model oscillators used to simulate the effects of electronic polarizability in the context of a classical molecular mechanics force field. Oscillation is the repetitive variation typically in Time, of some measure about a central value (often a point of Equilibrium) or between two or more different states Polarizability is the relative tendency of a charge distribution like the Electron cloud of an Atom or Molecule, to be distorted from its normal shape The term molecular mechanics refers to the use of Newtonian mechanics to model Molecular systems In the context of Molecular mechanics, a force field (also called a forcefield) refers to the functional form and Parameter sets used It is based on the Drude model of mobile electrons. The Drude model of Electrical conduction was proposed in 1900 by Paul Drude to explain the transport properties of Electrons in materials (especially metals Molecular mechanics models, commonly used for computational calculations such as structural minimization and molecular dynamics simulations, represent individual atoms or other particles as hard spheres that interact according to the laws of Newtonian mechanics. Molecular dynamics ( MD) is a form of Computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of History See also Atomic theory, Atomism The concept that matter is composed of discrete units and cannot be divided into arbitrarily tiny Classical mechanics is used for describing the motion of Macroscopic objects from Projectiles to parts of Machinery, as well as Astronomical objects These methods are often used in the computational study of proteins, nucleic acids, and other biomolecules. Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information A biomolecule is any organic Molecule that is produced by living Organisms including large Polymeric molecules such as Proteins
Most force fields in current practice use a fixed-charge model in which each atom in the simulation is assigned a single electric charge that does not change during the course of the simulation. This obviously cannot model induced dipoles or other electronic effects of a changing local environment. In physics there are two kinds of dipoles ( Hellènic: di(s- = two- and pòla = pivot hinge An electric dipole is a Drude particles are massless virtual sites carrying partial electric charge and attached to individual atoms via a harmonic spring. This article is about the harmonic oscillator in classical mechanics The spring constant and relative partial charges on the atom and associated Drude particle determine the extent to which the Drude particle responds to the local electrostatic field. In Mechanics, and Physics, Hooke's law of elasticity is an approximation that states that the amount by which a material body is deformed (the Electrostatics is the branch of Science that deals with the Phenomena arising from what seems to be stationary Electric charges Since Classical The movement of the Drude particle thus serves as a proxy for the changing distribution of the electric charge associated with the corresponding atom. [1]
The Drude particle method, and polarizable force fields in general, have not yet been widely applied due to their very high computational cost compared to the equivalent fixed-charge simulation. In the Drude model, this cost is largely due to the challenge in recalculating the local electrostatic field and repositioning the Drude particles at each time step; traditionally this is done using an iterative self consistent field (SCF) method, although a much more efficient method has been developed that assigns a very small mass to each Drude particle and applies a Lagrangian transformation. In Computational physics and Computational chemistry, the Hartree-Fock ( HF) method is an approximate method for the determination of the ground-state The Lagrangian, L of a Dynamical system is a function that summarizes the dynamics of the system [2] Water models incorporating Drude sites have also been developed[3] and refined for incorporation into a polarizable force field under development. Computational chemistry, classical water models are used for the simulation of Water clusters liquid water, and aqueous solutions with explicit solvent [4]
References
- ^ MacKerell AD. (2004). Empirical force fields for biological macromolecules: Overview and issues. J Comp Chem 25(13): 1584-1604.
- ^ Lamoureux G, Roux B. (2003). Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm. J Chem Phys 119(6):3025-3039.
- ^ Lamoureux G, MacKerell AD, Roux B. (2003). A simple polarizable model of water based on classical Drude oscillators. J Chem Phys 119(3):5185-97.
- ^ Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD. (2006). A polarizable model of water for molecular dynamics simulations of biomolecules. Chem Phys Lett 418:245-9.
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