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Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization
Author(s) -
Kundrot Craig E.,
Ponder Jay W.,
Richards Frederic M.
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.540120314
Subject(s) - volume (thermodynamics) , macromolecule , energy minimization , function (biology) , convergence (economics) , minification , energy (signal processing) , chemistry , lysozyme , thermodynamics , computational chemistry , mathematics , algorithm , crystallography , physics , mathematical optimization , statistics , biochemistry , evolutionary biology , biology , economics , economic growth
A numerical method for calculating the volume of a macromolecule and its first and second derivatives as a function of atomic coordinates is presented. For N atoms, the method requires about 0.3 N ln( N ) seconds of CPU time on a VAX‐8800 to evaluate the volume and derivatives. As a test case, the method was used to evaluate a pressure‐volume energy term in energy minimizations of the protein lysozyme at 1000 atm (1 atm = 1.013 × 10 5 Pa). R.m.s. gradients of 10 −4 kcal/mol/Å were obtained at convergence. The calculated structures exhibited pressure‐induced changes which were qualitatively similar to the changes observed in the 1000 atm structure determined by X‐ray crystallography.