Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model

2012 ◽  
Vol 8 (7) ◽  
pp. 2404-2411 ◽  
Author(s):  
Boris Aguilar ◽  
Alexey V. Onufriev
Keyword(s):  
Small Molecules ◽  
Solvation Energy ◽  
Efficient Computation ◽  
Generalized Born ◽  
Born Model ◽  
Generalized Born Model

The Gaussian Generalized Born model: application to small molecules

2007 ◽  
Vol 9 (35) ◽  
pp. 4913 ◽  
Author(s):  
J. A. Grant ◽  
B. T. Pickup ◽  
M. J. Sykes ◽  
C. A. Kitchen ◽  
A. Nicholls
Keyword(s):  
Small Molecules ◽  
Model Application ◽  
Generalized Born ◽  
Born Model ◽  
Generalized Born Model

Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field

2004 ◽  
Vol 108 (41) ◽  
pp. 16264-16270 ◽  
Author(s):  
William L. Jorgensen ◽  
Jakob P. Ulmschneider ◽  
Julian Tirado-Rives
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Generalized Born ◽  
Born Model ◽  
Generalized Born Model

VERIFICATION OF THE GENERALIZED BORN MODEL AT SHORT DISTANCES

2013 ◽  
Vol 13 (06) ◽  
pp. 1340020
Author(s):  
XIAOCHUAN TANG ◽  
YONG DUAN
Keyword(s):  
Analytical Solutions ◽  
Md Simulations ◽  
Solvation Energy ◽  
Implicit Solvent ◽  
Generalized Born ◽  
Simple Description ◽  
Born Model ◽  
Solvent Models ◽  
Potential Methods ◽  
Gb Model

The generalized Born (GB) model, one of the implicit solvent models, is widely applied in molecular dynamics (MD) simulations as a simple description of the solvation effect. In the GB model, an empirical function called the Still's formula, with the algorithmic simplicity, is utilized to calculate the solvation energy due to the polarization, termed as ΔG pol . Applications of the GB model have exhibited reasonable accuracy and high computational efficiency. However, there is still room for improvements. Most of the attempts to improve the GB model focus on optimizing effective Born radii. Contrarily, limited researches have been performed to improve the feasibility of the Still's formula. In this paper, analytical methods was applied to investigate the validity of the Still's formula at short distance. Taking advantage of the toroidal coordinates and Mehler–Fock transform, the analytical solutions of the GB model at short distances was derived explicitly for the first time. Additionally, the solvation energy was numerically computed using proper algorithms based on the analytical solutions and compared with ΔG pol calculated in the GB model. With the analysis on the deficiencies of the Still's formula at short distances, potential methods to improve the validity of the GB model were discussed.

scholarly journals Modification of the Generalized Born Model Suitable for Macromolecules

2000 ◽  
Vol 104 (15) ◽  
pp. 3712-3720 ◽  
Author(s):  
Alexey Onufriev ◽  
Donald Bashford ◽  
David A. Case
Keyword(s):  
Generalized Born ◽  
Born Model ◽  
Generalized Born Model
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