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Nonbonded Energy Terms

The options for the van der Waals and electrostatic energy terms are selected by an appropriate nbonds statement (see Section 3.2.1). Four combinations of nbonds options are possible. The first is TRUNcation in combination with CDIE , which uses Lennard-Jones and Coulomb functions. The second involves a switched van der Waals (VSWItch) and a shifted electrostatic function (SHIFt) in combination with CDIE. The third uses a switched van der Waals function (VSWItch) in combination with a switched electrostatic function (SWITch) and a

dielectric function (RDIE) . The fourth (REPEl

0) uses the so-called repel function, which is a purely repulsive function without attractive or electrostatic components. Any other combinations of the SHIFt, SWITch, VSHIft, VSWItch, CDIE, RDIE, TRUNCation and REPEl options are not possible and will produce an error message.

All nonbonded energy terms are truncated for atom pairs that are too close to each other (INHIbit option in the nonbonded statement, Section 3.2.1).

$\begin{displaymath} R \rightarrow {\rm max}(R, R_{inhibit}) \end{displaymath}$

(4.7)

This feature reduces numerical instabilities in the case of strained initial coodinates or close contacts during high simulation temperatures.

Subsections

Xplor-NIH 2025-03-21