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Next: Soft-Square Function Up: Choice of Restraining Functions Previous: Log Normal Function


Square-Well Function

For POTEntial=SQUAre-well, a square-well function is used:
\begin{displaymath} E_{NOE}^{class}= {\rm min}(ceil,S C) \Delta^{exp} \end{displaymath} (20.10)

where $\Delta$ is defined as

(20.11)


\begin{displaymath} \Delta = \left\{ \begin{array}{ll} R-(d+d_{plus}-d_{off}) &... ...d-d_{minus}-R) & \mbox{$R < d-d_{minus}$} \end{array} \right. \end{displaymath}

$S$ is the scale factor specified by the SCALe statement, $C$ is the scale factor specified by the SQCOnstant statement, and $d$, $d_{plus}$, 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 exponent $exp$ is specified by the SQEXponent statement and $d_{off}$ is specified by the SQOFfset value. The distance $R$ is defined in Section 20.2.


Xplor-NIH 2025-03-21