Energy Calculation between Selected Atoms
The constraints interaction statement tells
the empirical energy routines of XPLOR to compute
the energy between only two selected sets of atoms. It is convenient to
speak of these two selected sets as a double selection.
For twopoint
energy terms (such as covalent bonds and nonbonded interactions), the
energy is computed if one atom of the bond belongs to the
first selection and the other atom belongs to the second
selection. For threepoint terms (such as angles) and fourpoint terms
(such as dihedrals), the energy is computed if at least one atom
belongs to the first selection, at least one other atom belongs to the
second selection, and all atoms of the threepoint or
fourpoint term belong to at least one selection. The terms that are affected are
BOND, ANGL, DIHE, IMPR, VDW, ELEC, HBON, PVDW, and PELE (see Eq.
4.3). Other energy terms (e.g., Xray or NOE terms)
are not affected.
The statement can be issued several
times, thereby defining several double selections. In that case, the
total energy and the total forces are obtained by summing over
the different double selections. In addition,
when a double selection is defined,
the user may weight its contribution to the energy and forces
by attributing a weight to each individual energy term (bonds,
angles, etc.).
The constraints interaction statement also permits
one to build up a second energy function, , which
is useful for purposes of analysis. To do this, a second weight,
, is attributed to each individual energy term in
each double selection. This second weighting scheme does not
affect the forces or the dynamics of the system, but is purely
a tool for analysis.
The second energy function, , thus has the form

(4.26) 
The first sum is over the double selections ; the second is over the
empirical
energy terms: BOND, ANGL, DIHE, IMPR, VDW, ELEC, HBON, PVDW, and PELE.
This second energy function will appear as the “PERT" term in the
output and the energy symbols.
The invocation of the constraints statement will automatically erase
all previous double selections. To specify multiple
double selections one has to include them within the same constraints
statement, e.g.,
constraints
interaction=( segid "A" ) ( segid "A" )
interaction=( segid "B" ) ( segid "B" )
end
Subsections
XplorNIH 20240611