Nonbonding potentials

These functions allow- the nonbonded potential energy Lo turn off smoothly and systematically, removing artifacts caused by a truncated potential. With an appropriate switching function, the potential function is unaffected except m the region of the switch. 

HyperChem can also use a shifted nonbonded potential, where the nonbonded energy is modified by ... 

The OPLS form of electrostatic interactions is that of equation (26) on page 179. That is, it uses a charge-charge interaction just like AMBER. However, since the nonbonded potentials were developed... 

The matrix elements of the inactive electrons and the interaction between the active and inactive electrons can be approximated by expressing the corresponding potential surfaces as a quadratic expansion around the equilibrium values of the various internal coordinates, and by nonbonded potential functions for the interaction between atoms not bonded to each other or to a common atom ... 

The nonbonded potential can be described by an atom-atom interaction potential of the form used in eqs. (3.1) and (3.2). 

Schneider modified the calculation of the Grant-Cheney force that evaluates shielding by steric perturbations. The force F exerted at the C,.—H bond (C, being the carbon atom whose chemical shielding is to be computed) is calculated by an equation similar to that for a nonbonded potential ... 

Even within the limitations of fixed conformation, early force fields were deficient. The predicted unit cell dimensions were too small by more than 20 percent This situation was remedied by adjusting nonbonded potentials describing the fluorine-fluorine and carbon-fluorine interactions until predicted unit cell dimensions adequately reproduced experimentally measured values. This fitting was actually carried out using structural information from several polymers and was not an ad hoc parameterization for PTFE. It should also be pointed out that reproducing PTFE cell dimensions was a process of achieving an approximately correct interchain spacing for an approximate helix since the actual crystalline structure was not known at that time. Subsequently, it has become... 

The initial description of the model is simple, as shown in Figure 3. The atomic coordinates of any suitable structure can serve as the input trial structure, even including a wrong monomer residue. The polar coordinates are calculated from the trial structure, adjusted and modified as necessary, and then subjected to refinement in accordance with the selected list of variables, limits and constraints. Any set of standard values and nonbonded potential function parameters can be used. Hydrogen bonds can be defined as desired, variables can be coupled, and the positions of solvent molecules can be individually refined. Single and multiple helices are equally easily handled, as are a variety of space groups. 

The effect of the surface of the box on the solute is of major importance in the simulation of systems such as the one described here. The sudden cut-off of long-range nonbonded potentials at the box surface (beyond which is vacuum) would have an unnatural effect on the dynamics of the simulation. Only an extremely large system size could ensure a small influence of this surface effect on the solute. The computational cost of such a large system would be prohibitive. For this reason, periodic boundary conditions are used. The image of the simulation box is translated repeatedly to form an infinite lattice. When a particle in the simulation box moves, the image in all other translated boxes moves correspond-... 

A method for calculating the barriers to internal rotation has recently been proposed (Scott and Scheraga, 1965). It is based on the concept that the barrier arises from two effects, exchange interactions of electrons in bonds adjacent to the bond about which internal rotation occurs, and nonbonded or van der Waals interactions. The exchange interactions are represented by a periodic function, and the nonbonded interactions either by a Buckingham 6-exp or Lennard-Jones 6-12 potential function, the parameters of which are determined semi-empirically. (The parameters of the nonbonded potential energy functions are discussed in Section VB.)... 

A typical set of nonbonded potential functions (Scott and Scheraga, 1966c Ooi et al., 1967) obtained by the procedure described above is given in Table 16. Those of Brant and Flory (1965c) and of Brant et al. (1967), obtained by essentially the same procedure, differ somewhat from these because of the different values selected for the parameters of Table 15. Liquori (1966) has used a combination of Lennard-Jones and Buckingham functions, based primarily on work of Mason and Kreevoy (1955). 

Constants for Nonbonded Potential Functions (Scott and Scheraga, 1966c Ooi ef al., 1967)... 

Fig. 6. Nonbonded potential curves computed by Venkatachalam and Ramachandran...

Venkatachalam and Ramachandran (1967) have evaluated the various nonbonded potential functions described in Section VB, by using them to calculate nonbonded potential energy contours for the dipeptide glycyl-L-alanine and for helical poly-L-alanine. The functions considered were those of Brant and Flory (1965c), De Santis et al. (1965), Scott and... 

The Coulombic and vdW interactions are represented by the nonbonded potential term... 

If the nonbonded potential does not include the 1,3 vicinal intramolecular atom pairs, a stretch/bend cross-term is added of the form Er e = -i-kr e(r-r0)2-(0-0o>2... 

R. H. Boyd and co-workers have explored the application of anisotropic united-atom potentials in the MD simulation of liquid polyethylene. Their effort was motivated by recent evidence that united-atom CH2 Lennard-Jones nonbonded potentials are inadequate in some important respects. The use of the anisotropic potential gave good agreement between experiment and simulations for the equation of state P,V,T) and heat of vaporization. 

D. E. Williams and D. J. Houpt, Acta Crystallogr. B, 42, 286 (1986). Fluorine Nonbonded Potential Parameters Derived from Crystalline Perfluorocarbons. 

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