Cornell potential parameters

It can be seen from Table 1, that the description of the energy spectnnn using partial siuns (A +1 > 3) of the 1/n expansion is fairly accurate for the funnel potential. The axicuraey is enhanced as I increases, and it is especially high for nodeless states (IS, 2P,...). In the latter case, only three terms of the 1/n expansion ensure percent accuracy in energy and t/>(0) computations and properly reproduce [20] the charmonitnn spectrum if equation with Cornell potential parameters [23] is used. It is important that the above expressions allow one to perform with ease calculations for other potentials arising from QCD. 

Other potential functions differ in the way the potential is partitioned into various contributions representing intra and intermolecular interactions. Cornell and collaborators 300 proposed an approach to determine the force field parameters based as much as possible on ab initio calculations. In this work each biomolecular system is divided into small residua, for which geometry optimization can be performed by an ab initio method. Ab initio calculations give partial atomic charges on atoms and the equilibrium geometry, i.e. the equilibrium values for the bond lengths, and planar and dihedral angles. 

The last term in the formula (1-196) describes electrostatic and Van der Waals interactions between atoms. In the Amber force field the Van der Waals interactions are approximated by the Lennard-Jones potential with appropriate Atj and force field parameters parametrized for monoatomic systems, i.e. i = j. Mixing rules are applied to obtain parameters for pairs of different atom types. Cornell et al.300 determined the parameters of various Lenard-Jones potentials by extensive Monte Carlo simulations for a number of simple liquids containing all necessary atom types in order to reproduce densities and enthalpies of vaporization of these liquids. Finally, the energy of electrostatic interactions between non-bonded atoms is calculated using a simple classical Coulomb potential with the partial atomic charges qt and q, obtained, e.g. by fitting them to reproduce the electrostatic potential around the molecule. 

By integrating the Newtonian Equations of Motion, Molecular Dynamics simulations are able to describe the behavior of particles in a certain system within the observed period of time. The interaction of the atoms is described by the potential energy fxmction of the given force field [e.g. Amber (Cornell et al, 1995), CHARMM (Brooks et al., 1983), GROMOS (Scott et al., 1999), OPLS (Jorgensen Rives, 1988)]. Nowadays, there is an ongoing effort to ameliorate these parameters in a need for models being as less artificial as possible. 

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