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Understanding CONFLEX
Tutorials
The limit is increased to Limit 2 and all the conformers in the new
window (between Limit 1 and 2) are subjected to initial structures in
order of increasing energy. If local networks of conformers (LAN-a
and LAN-b) are not connected within the first window, LAN-b is
searched after LAN-c in the second window. A window width of 7
to 10 kcal/mol from the global minimum is generally sufficient to
achieve an exhaustive search of the first, chemically meaningful
window. Therefore, the variable limitation technique is a useful
strategy for keeping the search region under control in the universal
search.
Introduction
window (Limit 1) are used as the initial structures. During this
search, all the conformers are saved, even those with energies higher
than Limit 1.
To ensure exhaustive generation of all possible starting structures,
local perturbation is applied to every flexible part in the initial
structure. The following three modes of perturbation are designed to
mimic the elementary process in the thermal movements of a
molecule undergoing conformational change: corner flap and edge
flip for endocyclic parts, and stepwise rotation for acyclic parts.
Understanding
Customizing
If the perturbation cannot move the starting structure from the
territory to which it initially belonged, subsequent geometryoptimization will return it to the same structure. The territories of
similar conformers may be located in close vicinity in the
conformational space, constituting a local network of local
territories, and less similar conformers may be considered to belong
to different localities. Therefore, the method of perturbing an initial
structure to produce a candidate new conformer is also responsible
for the efficiency of search.
Basics
Local perturbation
Corner flap exploits the puckered feature of a ring structure, and
involves the movement of a corner ring-atom to the other side of the
local average plane. Two to four contiguous dihedral angles are
simultaneously changed along the ring. The advantages of corner
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Appendices
Corner flap