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Next: Log Normal Function Up: Choice of Restraining Functions Previous: Choice of Restraining Functions

Biharmonic Function

For POTEntial=BIHArmonic, a two-sided harmonic function is used:
\begin{displaymath} E_{NOE}^{class} = {\rm min}(ceil, \frac{SK_{b}T} {2c^{2}_{ij}}) \quad (R-d)^{2} \end{displaymath} (20.7)


\begin{displaymath} c_{ij} = \left\{ \begin{array}{ll} d_{minus} & \mbox{$R < d$} \\ d_{plus} & \mbox{$R > d$} \end{array} \right. \end{displaymath} (20.8)

where $S$ is the scale factor specified by the SCALe statement, $K_{b}$ is the Boltzmann constant, $T$ is the temperature specified by the TEMPerature statement, $ceil$ is specified by the CEILing statement, $d$, $d_{plus}$, and $d_{minus}$ are specified by the ASSIgn statement:

\begin{eqnarray*} {\tt assign \quad <selection> \quad <selection> } \quad d \quad d_{minus} \quad d_{plus} \end{eqnarray*}


The distance $R$ is defined in Section 20.2. The deviation $\Delta$ is defined as $\vert R-d\vert$.


Xplor-NIH 2025-03-21