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Molecular mechanics and the deformation of macromolecules: The use of a very short cutoff combined with a quadratic approximation
Author(s) -
Karfunkel H. R.
Publication year - 1987
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.540080210
Subject(s) - cutoff , quadratic equation , pairwise comparison , macromolecule , subspace topology , expression (computer science) , range (aeronautics) , molecular dynamics , deformation (meteorology) , space (punctuation) , statistical physics , physics , classical mechanics , computational chemistry , mathematics , quantum mechanics , chemistry , mathematical analysis , materials science , computer science , geometry , biochemistry , statistics , meteorology , composite material , programming language , operating system
An approximation to the molecular mechanical treatment of structural deformations of macromolecules is presented. The method is based on a partitioning of the conformational energy into three parts. The first part is covered by the condensed potential functions which absorb many short‐range nonbonding interactions. The second part consists of a few nonbonded interactions below a very short cutoff radius of 4 Å. The third part, consisting of the vast majority of pairwise interactions, is approximated by a quadratic expression confined to a subspace of the conformational space. A detailed computational example on LH‐RH, including an analysis of the errors resulting from other conventional approximation methods, is given. A comparison to the conventional cutoff approximation used in x‐ray refinement delivers a speedup factor of at least two orders of magnitude.
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