Potential energy nonbonded

Ifnited atom force fields (see Ifnited versiisAll Atom Forcehiclds" on page 28 ) arc sometimes used for bioraoleciiles to decrease the number of nonbonded in teraction s and the computation time. Another reason for using a simplified poten tial is to reduce the dimensionality of the potential energy surface. This, in turn, allows for more samples of the surface. 

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. 

Force field calculations often truncate the non bonded potential energy of a molecular system at some finite distance. Truncation (nonbonded cutoff) saves computing resources. Also, periodic boxes and boundary conditions require it. However, this approximation is too crude for some calculations. For example, a molecular dynamic simulation with an abruptly truncated potential produces anomalous and nonphysical behavior. One symptom is that the solute (for example, a protein) cools and the solvent (water) heats rapidly. The temperatures of system components then slowly converge until the system appears to be in equilibrium, but it is not. 

The classical force field represents the potential energy of a polymer chain, made of N atoms with coordinates given by the set r, as a sum of nonbonded interactions and contributions from all bond, valence bend, and dihedral interactions ... 

The role of the potential energy is taken by the Dyana target function [8, 28] that is defined such that it is zero if and only if all experimental distance constraints and torsion angle constraints are fulfilled and all nonbonded atom pairs satisfy a check for the absence of steric overlap. A conformation that satisfies the constraints more closely than another one will lead to a lower target function value. The exact definition of the Dyana target function is ... 

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