Regularization
XPLOR can regularize coordinates that are
obtained by distance geometry embedding by minimizing
the coordinates against an effective energy term (DG) that represents
all upper and lower bounds in the distance geometry
bounds matrix. The bounds matrix has to be stored
in memory using the STOREBounds statement prior to
invoking the DG energy term. The atoms
that should be restrained have to be defined through the
SELEction statement. The DG term is defined as

(37.1) 
where
is the scale factor specified by the SCALe statement, is the
exponent defined by the EXPOnent statement,
is the upper bounds,
is the lower bounds
generated by the initialization stage of distance
geometry, and the sum
goes over all atoms , that are selected by the
selection statement.
The DG energy term is turned on by using the flag statement
(see Section 4.5). Normally, all other
energy terms should be turned off when using the DG
term. However, for defining the bounds matrix initially,
the other energy terms should be turned on, because bounds
are computed only for the activated energy terms. Then,
after storing the bounds matrix, all other energy terms
should be turned off and the DG energy term turned on.
Energy minimization,
molecular dynamics, or any other energy calculation can be
performed with the DG energy term.
XplorNIH 20231110