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Molecular Modeling Basics - Jan H. Jensen - Google книги

Anderen bekeken ook. Kumosinski Molecular Modeling 46, Andreas Kukol Molecular Modeling of Proteins , Kukol, Andreas Molecular Modeling of Proteins , Kenny B. Lipkowitz Reviews in Computational Chemistry , Bekijk de hele lijst.

The electrostatic interactions are computed based on Coulomb's law. Atoms are assigned coordinates in Cartesian space or in internal coordinates , and can also be assigned velocities in dynamical simulations. The atomic velocities are related to the temperature of the system, a macroscopic quantity.

Molecular Modeling Basics

The collective mathematical expression is termed a potential function and is related to the system internal energy U , a thermodynamic quantity equal to the sum of potential and kinetic energies. Methods which minimize the potential energy are termed energy minimization methods e. This function, referred to as a potential function , computes the molecular potential energy as a sum of energy terms that describe the deviation of bond lengths, bond angles and torsion angles away from equilibrium values, plus terms for non-bonded pairs of atoms describing van der Waals and electrostatic interactions.

The set of parameters consisting of equilibrium bond lengths, bond angles, partial charge values, force constants and van der Waals parameters are collectively termed a force field. Different implementations of molecular mechanics use different mathematical expressions and different parameters for the potential function.

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The method, termed energy minimization, is used to find positions of zero gradient for all atoms, in other words, a local energy minimum. Lower energy states are more stable and are commonly investigated because of their role in chemical and biological processes. A molecular dynamics simulation, on the other hand, computes the behaviour of a system as a function of time.

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Integration of Newton's laws of motion, using different integration algorithms, leads to atomic trajectories in space and time. The force on an atom is defined as the negative gradient of the potential energy function. The energy minimization method is useful to obtain a static picture for comparing between states of similar systems, while molecular dynamics provides information about the dynamic processes with the intrinsic inclusion of temperature effects.

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The basic concepts of molecular modeling.

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Molecular Modelling by Dr Marek Szczerba

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