Coulomb interactions nonbonded

The nonbonded interactions commonly consist of a sum of two-body repulsion and dispersion energy terms between atoms that are often of the Lennard-Jones form in addition to the energy from the interactions between fixed partial atomic or ionic charges (Coulomb interaction)... 

Next in the list, but of course not of lesser importance among the interactions between nonbonded atoms, is the Coulomb interaction of effective charges residing on atoms in the molecule ... 

Nonbonding interactions play a major role in determining the three-dimensional structure of a molecule. Such interactions are composed of repulsive and attractive contributions, such as van der Waals repulsion, London dispersion forces, coulombic interactions, and delocalizations of electrons due to the through-space interactions between atomic orbitals. 

Nonbonded interacations invovle a sum of van der Waals (VDW) interactions and coulombic interactions. The coulombic term accounts for charge-charge interactions. 

In force fields such as AMBERS or CHARMM designed for large biological molecules, the Coulombic interaction in Eq. [10] is sometimes modified by use of a distance-dependent dielectric constant. Another modification of Eqs. [10] and [11] is utilized in force fields designed for hydrocarbons and concerns the internuclear distance R, in the van der Waals interaction (the non-Coulom-bicpart of Eq. [10]) when one of the nonbonded atoms is a hydrogen. 

The main problem in a biological system is that the nonbonded terms are roughly proportional to the square of the number of atoms. Thus, in the case of a small membrane protein embedded in a natnral membrane with a typical number of atoms of around 25 000, one must compute roughly 625 000 000 Van der Waal s and Coulomb interactions. 

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