mmdg {<mmdg-statement>} end
<mmdg-statement> :==
writebounds=<filename>
Smoothed bounds matrices are written to this file, no
metrization or embedding are performed.
readbounds=<filename>
Read smoothed bounds matrices from this file, then metrization
and embedding are performed.
storebounds
Smoothed bounds matrices are stored in memory, no metrization
or embedding are performed. This is required for subsequent
calls with recallbounds or for using the dg energy term.
recallbounds
Recall smoothed bounds matrices from memory, metrization and
embedding are then performed.
reference=parameter|coordinate
Use parameters or coordinates to fill distances for bonds,
angles, and unique dihedrals or impropers. Takes information
from reference coordinates for refe=coordinate.
metrization <atom-selection> <real>
Atom selection and number of picked subset of atoms that are
used for metrization. Bound smoothing is applied to other
atoms. Default=(none)
random|ordered
Mutually exclusive options for ordered or random metrization.
All steps of distance geometry calculations (initialization,
metrization, smoothing, and embedding) are executed by default
unless storebounds, writebounds, recallbounds or readbounds are
specified.
For automatic pseudoatom correction a template coordinate set
must be present in the reference coordinate set (refx, refy, refz).