Variational electrostatic projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations.
New methods for the calculation of electrostatic interactions between the active dynamical region and surrounding external solvated macromolecular environment in hybrid quantum mechanical/molecular mechanical (QM/MM) simulations are presented. The variational electrostatic projection (VEP) method, and related variational reverse-mapping procedure (VEP-RVM) utilize an expansion in Gaussian surface elements for representation of electrostatic interactions. The use of a discretized surface that surrounds the active dynamical region greatly reduces the number of interactions with the particles of the external environment. The methods are tested on two catalytic RNA systems: the hammerhead and the hairpin ribozymes. It is shown that with surface elements numbering from 302 to 1202 points the direct VEP and VEP-RVM methods are able to obtain relative force errors in the range of 0.5-0.05% and 0.09-0.0001%, respectively, using a 4.0 A projection buffer. These results are encouraging and provide an essential step in the development of new variational macromolecular solvent-boundary methods for QM/MM calculations of enzyme reactions.
Gregersen
Brent A
BA
Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA.
York
Darrin M
DM
D003198:Computer Simulation; D046911:Macromolecular Substances / Q000737:chemistry; D008956:Models, Chemical; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity
D046911:Macromolecular Substances; D012997:Solvents