A charge-scaling implementation of the variational electrostatic projection method.
Two new charge-scaling methods for efficient modeling of the solvated macromolecular environment in hybrid QM/MM calculations of biological reactions are presented. The methods are extensions of the variational electrostatic projection (VEP) method, and allows a subset of atomic charges in the external environment to be adjusted to mimic, in the active dynamical region, the electrostatic potential and field due to the large surrounding macromolecule and solvent. The method has the advantages that it offers improved accuracy, does not require the use of a three-dimensional grid or auxiliary set of fitting points, and requires only minor molecular simulation code modifications. The VEP-cs and VEP-RVM+cs methods are able to attain very high accuracy (relative force errors of 10(-7) or better with appropriate choice of control parameters), and take advantage of a recently introduced set of high-order discretization schemes and Gaussian exponents for boundary element solvation and VEP methods. The methods developed here serve as potentially powerful tools in the arsenal of computational techniques used in multiscale computational modeling problems.
Gregersen
Brent A
BA
Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA.
York
Darrin M
DM
D001704:Biopolymers / Q000737:chemistry; D008958:Models, Molecular; D016337:RNA, Catalytic / Q000737:chemistry; D012997:Solvents; D055672:Static Electricity
D001704:Biopolymers; D016337:RNA, Catalytic; D012997:Solvents; C427204:hammerhead ribozyme