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Applications of simulated annealing to the conformational analysis of flexible molecules
Author(s) -
Wilson Stephen R.,
Cui Weili,
Moskowitz Jules W.,
Schmidt Kevin E.
Publication year - 1991
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540120307
Subject(s) - annealing (glass) , molecule , simulated annealing , computational chemistry , materials science , chemistry , chemical physics , computer science , crystallography , algorithm , composite material , organic chemistry
We describe in this article our solution to the global minimum problem which uses the simulated annealing algorithm of Kirkpatrick. This method is a Metropolis ( e ‐Δ E / kT ) Monte Carlo sampling of conformation space with simultaneous constraint of the search by lowering the temperature T so that the search converges on the global minimum. The Anneal‐Conformer program has been extensively tested with peptides and organic molecules using either the Amber or MM2 force fields. A history file of the simulated annealing process allows reconstruction of the random walk in conformation space for subsequent examination. Thus plots of distance and dihedral angle changes during the search for the global minimum can be examined to deduce molecular shape and flexibility. A separate program Conf‐Gen reads the history file and extracts all low energy conformations visited during the run.