Function, nonbonded potential

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. 

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 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. 

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)... 

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... 

Determines hydrogen-bonding energies Generates an energy vs. rotation angle plot Lists all atomic coordinates Allows modification of Lennard-Jones, nonbonded potential function parameters Lists all low energy conformers Performs multi-dimensional minimization Performs random type scan of conformational hyperspace... 

Table II. Values for the Nonbonded Potential Function (cont d.)...

The functional form of such a nonbonded potential, Vnb, has been discussed by a number of authors (Kitaigorodsky, 1961, 1973, 1978 Williams, 1981). It is composed of attractive. Van, and repulsive, Vrep, parts ... 

D. E. Williams, Topics Current Phys., 26, 3 (1981). Transferable Empirical Nonbonded Potential Functions. 

In Section 4.2 we describe how nonbonded potentials are derived for polymer systems, but for now we list some of the isotropic functions used for their representation. Of these, two common forms are the Buckingham potential... 

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