Paper Citing NAMD - Abstract
Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro
Generalized Born forces: Surface integral formulation
JOURNAL OF CHEMICAL PHYSICS, 138 Art. No. 054112, FEB 7 2013
Generalized Born (GB) models offer a convenient alternative to Poisson-Boltzmann based models. In the last decade, the GB radii computed based on the exact results obtained for a charge embedded in a conducting sphere have proven to be accurate also for the complex molecular shapes of proteins. The surface integral formulation of the theory has been much less explored than the volume integral formulation. In this work, we provide the exact equations for the GB solvation forces in the surface integral formulation, which are non-trivial due to the non-negligible dependence of GB radii on atomic positions and due to the discontinuity in the derivative of the solvent accessible surface point positions with respect to atomic positions. The equations derived here provide a useful reference for developing faster approximations. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4789537]
