Theory and applications of the generalized born solvation model in macromolecular simulations

TLDR

Generalized Born models enable inclusion of key thermodynamic aspects of aqueous solvation in simulations that omit explicit solvent molecules. The study aims to detail the implementation and parallelization of the Generalized Born model within the AMBER molecular modeling code. The authors compare GB (and GB plus a surface‑area hydrophobic term) results to explicit solvent simulations for a 10‑base‑pair DNA oligomer and the 108‑residue protein thioredoxin. A modest parameter tweak strengthens NH–O and NH–N internal hydrogen bonds, bringing GB results closer to explicit solvent, while timing and energy stability data suggest the model is suitable for larger macromolecular systems and longer simulations. © 2001 John Wiley & Sons, Inc., Biopolymers (Nucleic Acid Sci) 56: 275–291.

Abstract

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 NHO and NHN 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