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Molecular Mechanics - Biomatics.org

Molecular Mechanics

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Molecular mechanics uses Newtonian mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields. Molecular mechanics can be used to study small molecules as well as 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 a single 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

Variations on this theme are possible; for example, many simulations have historically used a "united-atom" representation in which methyl and methylene groups were represented as a single particle, and large protein systems are commonly simulated using a "bead" model that assigns two to four particles per amino acid.

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