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Analysis of the Nonbonded Energy Terms

The distance statement allows one to analyze the nonbonded interactions, such as inter- or intramolecular close contacts. The nonbonded distances are analyzed as provided by the nonbonded list routines. Selected parts of the nonbonded list may be printed by specifying an upper and lower cutoff and atom selections. All nonbonded distances between the first and second set of atoms that satisfy the cutoff criteria are printed. (See Section 3.2.1 for nonbonded list parameters and options.) It should be noted that the distance statement is most useful for checking contacts between molecules. It can also be used to produce a distance matrix. However, the distance statement is not very flexible when certain averages of distances are required. (See Section 6.4 for a much more flexible approach to computing and plotting a distance matrix.)

Subsections

Xplor-NIH 2025-03-21