title: Quantitative Assessment of Electrostatic Embedding in Density Functional Theory Calculations of Biomolecular Systems.
abstract: We evaluate the accuracy of density functional theory quantum calculations of biomolecular subsystems using a simple electrostatic embedding scheme. Our scheme is based on dividing the system of interest into a primary and secondary subsystem. A finite difference discretization of the Kohn-Sham equations is used for the primary subsystem, while its electrostatic environment is modeled with a simple one-electron potential. Force-field atomic partial charges are used to generate smeared Gaussian charge densities and to model the secondary subsystem. We illustrate the utility of this approach with calculations of truncated dipeptide chains. We analyze quantitatively the accuracy of this approach by calculating atomic forces and comparing results with full QM calculations. The impact of the choice made in terminating dangling bonds at the frontier of the QM region is also investigated.
authors.affiliation: Center for Applied Scientific Computing, and Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94551.
authors.forename: J-L
authors.initials: JL
authors.lastname: Fattebert
authors.affiliation: Center for Applied Scientific Computing, and Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94551.
authors.forename: R J
authors.initials: RJ
authors.lastname: Law
authors.affiliation: Center for Applied Scientific Computing, and Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94551.
authors.forename: B
authors.initials: B
authors.lastname: Bennion
authors.affiliation: Center for Applied Scientific Computing, and Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94551.
authors.forename: E Y
authors.initials: EY
authors.lastname: Lau
authors.affiliation: Center for Applied Scientific Computing, and Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94551.
authors.forename: E
authors.initials: E
authors.lastname: Schwegler
authors.affiliation: Center for Applied Scientific Computing, and Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94551.
authors.forename: F C
authors.initials: FC
authors.lastname: Lightstone