Electrostatic forces nonbonded interactions

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

Parallel molecular dynamics codes are distinguished by their methods of dividing the force evaluation workload among the processors (or nodes). The force evaluation is naturally divided into bonded terms, approximating the effects of covalent bonds and involving up to four nearby atoms, and pairwise nonbonded terms, which account for the electrostatic, dispersive, and electronic repulsion interactions between atoms that are not covalently bonded. The nonbonded forces involve interactions between all pairs of particles in the system and hence require time proportional to the square of the number of atoms. Even when neglected outside of a cutoff, nonbonded force evaluations represent the vast majority of work involved in a molecular dynamics simulation. 

MOMEC is a force field for describing transition metal coordination compounds. It was originally parameterized to use four valence terms, but not an electrostatic term. The metal-ligand interactions consist of a bond-stretch term only. The coordination sphere is maintained by nonbond interactions between ligands. MOMEC generally works reasonably well for octahedrally coordinated compounds. 

Although interactions between vicinal atoms are nominally treated as nonbonded interactions, most of the force fields treat these somewhat differently from normal 1-5 and greater nonbonded interactions. HyperChem allows each of these nonbonded interactions to be scaled down by a scale factor <1.0 with AMBER or OPLS. For BlO-t the electrostatic may be scaled and different parameters may be used for 1 van der Waals interactions. Th e AMBER force field, for exam p le, norm ally u ses a scalin g factor of 0.5 for both van der Waals and electrostatic interactions. 

The mechanism of charge reorganization attending the interconversion of geometric isomers due to nonbonded interaction effects has already been discussed before1. The electrostatic effect can be thought of as the effect which forces the distribution of charge in such a way that electrostatic repulsions are minimized. 

EAS (Engler, Andose, Schleyer) [184] is quite an old force field designed to model alkanes exclusively. The harmonic potential is used for the bond stretching and cubic anharmonic for the valence angle bending. No out of plane, electrostatic or cross terms are included. The nonbonded interactions are represented by the Buchingham potential. 

ESFF has been designed to be universal [187]. The Morse potential is employed for bond stretching, the potential quadratic in the cosine of the valence angles for their bending and the harmonic potential for the out of plane force field. The 6-9 with the charge based electrostatic potential is used for nonbonding interactions. No cross terms are involved. 

The valence interactions consist of bond stretching, bond angle bending, and dihedral angle torsion, active in nearly all force-fields for covalent systems. The nonbonded interactions consist of van der Waals, electrostatic and hydrogen bond terms, and the form of each expression depends on the particular force-field [67,62]. 

The zeolite framework was described by a specific force field developed by van Santen et al. [11] while the hydrocarbon molecules and their interaction among themselves and with the zeolite lattice were described by the generic force field Drdding n [12]. All the internal coordinates of the alkane molecules were allowed to fully relax. The nonbonded interactions (electrostatic and van der Waals) were computed for aU atoms within a cutoff-radius of 12A. Periodic boundary conditions were imposed along the three axes of the zeolite model to simulate an infinite crystal. 

The motions of proteins are usually simulated in aqueous solvent. The water molecules can be represented either explicitly or implicitly. To include water molecules explicitly implies more time-consuming calculations, because the interactions of each protein atom with the water atoms and the water molecules with each other are computed at each integration time step. The most expensive part of the energy and force calculations is the nonbonded interactions because these scale as 77 where N is the number of atoms in the system. Therefore, it is common to neglect nonbonded interactions between atoms separated by more than a defined cut-off ( 10 A). This cut-off is questionable for electrostatic interactions because of their 1/r dependence. Therefore, in molecular dynamics simulations, a Particle Mesh Ewald method is usually used to approximate the long-range electrostatic interactions (71, 72). 

Nonbonded interactions consist of van der Waals (VDW) and electrostatic potentials. Examples of the valence force field approach include UFF or DREIDING [54], MM2/MMP2 [55], AMBER [56], and CHARMM [57]. The parameters of the potentials can be determined from either experiments or ab initio quantum chemical methods [58]. 

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