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Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: A robust and efficient algorithm
Author(s) -
Kinoshita Masahiro,
Okamoto Yuko,
Hirata Fumio
Publication year - 1997
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/(sici)1096-987x(19970730)18:10<1320::aid-jcc6>3.0.co;2-p
Subject(s) - jacobian matrix and determinant , robustness (evolution) , matrix (chemical analysis) , molecule , algorithm , set (abstract data type) , chemistry , statistical physics , computer science , computational chemistry , mathematics , physics , biochemistry , organic chemistry , chromatography , gene , programming language
We have developed an algorithm for solving the referenceinteraction site model (RISM) equations for water near a solute moleculewith many atomic sites (interaction sites). It is a hybrid of theNewton–Raphson and Picard methods and is judiciously constructed.Various considerations are given so that the computer time can be saved asmuch as possible. The robustness and high efficiency of the algorithm hasbeen demonstrated for calculating hydration free energies of Met‐enkephalin(a peptide with 75 sites) with different conformations. The Jacobian matrixis treated as part of the input data, and it has been found that the samematrix can be used for a considerably large set of different conformationsof the solute molecule. © 1997 John Wiley & Sons, Inc. J ComputChem 18: 1320–1326, 1997