Molecular mechanics force field definition

The original molecular-mechanics force field was developed by Allinger, and is generally referred to as MM. You should read the definitive text by Burkert and Allinger (1982) for more details. This model was followed by the MM2 model (Allinger, 1977), and I thought that you might like to read the synopsis. 

In contrast to molecular mechanics force fields, modern semiempirical methods are classified as an SCF electron-structure theory (wavefunction-based) method [12]. Older (pre-HF) semiempirical approaches such as extended Hvickel theory, which can be classified as a one-electron effective Hamiltonian approach, involve drastic approximations but rely on the researcher s intuition and ability to extrapolate from simple computations to meaningful chemistry. This method is not used much these days but still plays a role in determining the band structures of organic polymers, most of which are carbon-rich by definition [13]. 

The atomic radii may be further refined to improve the agreement between experimental and theoretical solvation free energies. Work on this direction has been done by Luque and Orozco (see [66] and references cited therein) while Barone et al. [67] defined a set of rules to estimate atomic radii. Further discussion on this point can be found in the review by Tomasi and co-workers [15], It must be noted that the parameterization of atomic radii on the basis of a good experiment-theory agreement of solvation energies is problematic because of the difficulty to separate electrostatic and non-electrostatic terms. The comparison of continuum calculations with statistical simulations provides another way to check the validity of cavity definition. A comparison between continuum and classical Monte Carlo simulations was reported by Costa-Cabral et al. [68] in the early 1980s and more recently, molecular dynamics simulations using combined quantum mechanics and molecular mechanics (QM/MM) force-fields have been carried out to analyze the case of water molecule in liquid water [69],... 

There is a tendency to use the term molecular mechanics (MM) as opposite to quantum mechanics, therefore including all classical dynamics methods, such as energy minimization, Monte Carlo, and molecular dynamics. Sometimes it is used to describe only the energy minimization method using empirical force field (potential) or it is even used to refer to the quantum mechanical method specifically, emphasizing its use for molecular motion. Nevertheless, we will focus on the second definition of molecular mechanics (43-45). In this approach, a molecule is viewed as a collection of particles (atoms) held together by simple harmonic or elastic forces. Such forces are defined in terms of potential energy... 

The rhodopsin protein problem An all-atom rhodopsin protein was set in a solvated lipid bilayer described via the Chemistry at Harvard Molecular Mechanics (CHARMM) force field. Long-range coulomb interactions were described via the particle-particle mesh. SHAKE constraints were applied to the system for the definitions of the force field and constraints. Further, the model consisted of counter ions with a reduced amount of water the effect was to have a total system with 32,000 atoms that was simulated for 100 time steps. This simulation was performed at a constant pressure and temperature with an LJ force cutoff of 10.0 Angstroms. In this problem, the total number of neighbors per atom was 440 within this force cutoff More information about the benchmark problem can be found at http //lammps.sandia.gOv/bench.html rhodo... 

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