Use of classical mechanics to model molecular systems
A force field is used to minimize the bond stretching energy of this ethane molecule.
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.
and 23 Related for: Molecular mechanics information
Molecularmechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy...
predominantly used for molecularmechanics calculations. GPU – GPU accelerated I – Has interface Imp – Implicit water MC – Monte Carlo MD – Molecular dynamics Min...
other programs are now in use. At the same time, the methods of molecularmechanics, such as MM2 force field, were developed, primarily by Norman Allinger...
chemistry approach). Molecularmechanics is one aspect of molecular modelling, as it involves the use of classical mechanics (Newtonian mechanics) to describe...
Comparison of software for molecularmechanics modeling List of molecular graphics systems List of software for Monte Carlo molecular modeling List of software...
of forces are essential parts of force fields frequently used in molecularmechanics. The first reference to the nature of microscopic forces is found...
molecule. The study of molecules by molecular physics and theoretical chemistry is largely based on quantum mechanics and is essential for the understanding...
chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems...
chemistry, molecular orbital theory (MO theory or MOT) is a method for describing the electronic structure of molecules using quantum mechanics. It was proposed...
flows, or molecular flows on nano scale. Those problems for which the continuum hypothesis fails can be solved using statistical mechanics. To determine...
chemistry, i.e., the application of quantum mechanics to problems in chemistry. Other major components include molecular dynamics, statistical thermodynamics...
electrochemistry, statistical mechanics, spectroscopy, and more recently, astrochemistry. Physical chemistry has large overlap with molecular physics. Physical chemistry...
Quantum chemistry calculations and molecularmechanics simulations (molecular modeling in terms of classical mechanics) are among beneficial applications...
for molecularmechanics modeling Comparison of force field implementations Molecular dynamics Molecular geometry Molecular design software Molecular mechanics...
electrochemistry, statistical mechanics, spectroscopy, and more recently, astrochemistry. Physical chemistry has large overlap with molecular physics. Physical chemistry...
The ONIOM (short for 'Our own N-layered Integrated molecular Orbital and Molecularmechanics') method is a computational approach developed by Keiji Morokuma...
with explicit solvent. The models are determined from quantum mechanics, molecularmechanics, experimental results, and these combinations. To imitate a...
Mechanics (from Ancient Greek: μηχανική, mēkhanikḗ, lit. "of machines") is the area of physics concerned with the relationships between force, matter...
of nucleic acid simulation software List of software for molecularmechanics modeling Molecular design software Protein design bio.tools, finding more tools...
Global Information