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:

& & {\tt assign \quad <selection> \quad <selection> }
\quad d ...
...n \quad <selection> \quad <selection> }
\quad 0 \quad 0 \quad 0

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

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


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.

Xplor-NIH 2023-11-10