Energy Calculation between Selected Atoms

The constraints interaction statement tells the empirical energy routines of X-PLOR 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 two-point 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 three-point terms (such as angles) and four-point 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 three-point or four-point 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., X-ray 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, $V_{total}$, which is useful for purposes of analysis. To do this, a second weight, $v_{pk}$, 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, $V_{total}$, thus has the form

V_{TOTAL} = \sum_{p=1}^{N} [ \sum_{k} w^p_{k} E_{k} ]
\end{displaymath} (4.26)

The first sum is over the $N$ 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.,

  interaction=( segid "A" ) ( segid "A" ) 
  interaction=( segid "B" ) ( segid "B" ) 

Xplor-NIH 2023-11-10