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Concept
Mécanique moléculaire
Résumé
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
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)
Bonded interactions are treated as springs with an equilibrium distance equal to the experimental or calculated bond length
Variants on this theme are possible. 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.
The following functional abstraction, termed an interatomic potential function or force field in chemistry, calculates the molecular system's potential energy (E) in a given conformation as a sum of individual energy terms.
where the components of the covalent and noncovalent contributions are given by the following summations:
The exact functional form of the potential function, or force field, depends on the particular simulation program being used. Generally the bond and angle terms are modeled as harmonic potentials centered around equilibrium bond-length values derived from experiment or theoretical calculations of electronic structure performed with software which does ab-initio type calculations such as Gaussian. For accurate reproduction of vibrational spectra, the Morse potential can be used instead, at computational cost.
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