Force field methods electrostatic energies

Molecular Mechanics. Molecular mechanics (MM), or empirical force field methods (EFF), are so called because they are a model based on equations from Newtonian mechanics. This model assumes that atoms are hard spheres attached by networks of springs, with discrete force constants. The force constants in the equations are adjusted empirically to repro duce experimental observations. The net result is a model which relates the "mechanical" forces within a structure to its properties. Force fields are made up of sets of equations each of which represents an element of the decomposition of the total energy of a system (not a quantum mechanical eneigy, but a classical mechanical one). The sum of the components is called the force field eneigy, or steric energy, which also routinely includes the electrostatic eneigy components. Typically, the steric energy is expressed as... 

In section II we focused on an accurate description of electrostatic interactions between solute and solvent. Although these interactions accormt for the largest parts of the free energy of solvent, other interactions may contribute as well. These interactions, due to dispersion and repulsion, were studied by Curutchet et al Amoville and Mennucci had earlier developed a formalism for including these interactions in the polarizable continuum model and Curutchet et al. tested it on a larger set of solvent-solute systems for which they also calculated these interactions with force-field methods. 

The EFP method attempts to overcome this parameterization problem by including electrostatics and polarization from first principles. This represents a considerable departure from the traditional MM potentials used in biomolecular simulations. The electrostatic energy remains an approximation, however, as the multipole expansions in Ueie are left uncorrected for the effects of charge penetration (C/pen). This penetration energy, Upen, is then implicit in Urep. Thus a limitation that is characteristic of all force-field methods, from the crudest MM to the most sophisticated QM/MM, is a certain lack of generality, i.e., there are arbitrary parameters that have to be refined and fitted for a particular application. 

AMI AMBER A Program for Simulation of Biological and Organic Molecules CHARMM The Energy Function and Its Parameterization Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Divide and Conquer for Semiempirical MO Methods Electrostatic Catalysis Force Fields A General Discussion Force Fields CFF GROMOS Force Field Hybrid Methods Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Methods Mixed Quantum-Classical Methods MNDO MNDO/d Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Parameterization of Semiempirical MO Methods PM3 Protein Force Fields Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mecha-nics/Molecular Mechanics (QM/MM) SINDOI Parameterization and Application. 

Empirical conformational energy program for peptides (ECEPP) is the name of both a computer program and the force field implemented in that program. This is one of the earlier peptide force fields that has seen less use with the introduction of improved methods. It uses three valence terms that are fixed, a van der Waals term, and an electrostatic term. 

To make an accurate FEP calculation, a good description of the system is required. This means that the parameters for the chosen force field must reproduce the dynamic behaviour of both species correctly. A realistic description of the environment, e.g. size of water box, and the treatment of the solute-solvent interaction energy is also required. The majority of the parameters can usually be taken from the standard atom types of a force field. The electrostatic description of the species at both ends of the perturbation is, however, the key to a good simulation of many systems. This is also the part that usually requires tailoring to the system of interest. Most force fields require atom centered charges obtained by fitting to the molecular electrostatic potential (MEP), usually over the van der Waals surface. Most authors in the studies discussed above used RHF/6-31G or higher methods to obtain the MEP. 

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