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Theory and applications of the generalized born solvation model in macromolecular simulations
Author(s) -
Tsui Vickie,
Case David A.
Publication year - 2000
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/1097-0282(2000)56:4<275::aid-bip10024>3.0.co;2-e
Subject(s) - solvation , chemistry , implicit solvation , hydrogen bond , solvent , macromolecule , aqueous solution , computational chemistry , solvent models , molecule , solvent effects , statistical physics , molecular dynamics , chemical physics , thermodynamics , organic chemistry , physics , biochemistry
Generalized Born (GB) models provide an attractive way to include some thermodynamic aspects of aqueous solvation into simulations that do not explicitly model the solvent molecules. Here we discuss our recent experience with this model, presenting in detail the way it is implemented and parallelized in the AMBER molecular modeling code. We compare results using the GB model (or GB plus a surface‐area based “hydrophobic” term) to explicit solvent simulations for a 10 base‐pair DNA oligomer, and for the 108‐residue protein thioredoxin. A slight modification of our earlier suggested parameters makes the GB results more like those found in explicit solvent, primarily by slightly increasing the strength of NHO and NHN internal hydrogen bonds. Timing and energy stability results are reported, with an eye toward using these model for simulations of larger macromolecular systems and longer time scales. © 2001 John Wiley & Sons, Inc. Biopolymers (Nucleic Acid Sci) 56: 275–291, 2001