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NIH: National Institute of Diabetes and Digestive and Kidney Diseases NIH: National Institute of Diabetes and Digestive and Kidney Diseases

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Next: 3D NOE-NOE Function Up: Choice of Restraining Functions Previous: Soft-Square Function

Symmetry Function

For POTEntial=SYMMetry, a soft-square function (Eq. 20.12) is used to restrain signed distance differences to specified values. The two distances are specified by a pair of ASSIgn statements:

\begin{eqnarray*}
& & {\tt assign \quad <selection> \quad <selection> }
\quad d ...
...n \quad <selection> \quad <selection> }
\quad 0 \quad 0 \quad 0
\end{eqnarray*}


The second distance of a given pair of distances is subtracted from the first; the distance difference can have negative values. The functional form is similar to the soft-square function (Section 20.3.4), except that the switching region is symmetrically arranged around the ideal distance difference (i.e., the program switches to the soft asymptote for $R > d+d_{plus}-d_{off} + r_{sw}$ as well as for $R < d-d_{minus} - r_{sw}$) and $\Delta$ is defined as

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


  (20.13)

where $D$ denotes the distance difference $R_1 - R_2$ between the two assigned distances. The distances $R_1$ and $R_2$ are obtained by various averaging methods as described in Section 20.2.



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