"Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution"Bernhard Egwolf and Paul Tavan
J. Chem. Phys. 120, 2056-2068 (2004)
We extend our continuum description of solvent dielectrics in molecular-dynamics (MD)
simulations [B. Egwolf and P. Tavan, J. Chem. Phys. 118,
2039-2056, (2003)], which has provided an efficient and accurate solution
of the Poisson equation, to ionic solvents as described by the linearized
Poisson-Boltzmann (LPB) equation. We start with the formulation of a general theory
for the electrostatics of an arbitrarily shaped molecular system,
which consists of partially charged atoms and is embedded in an LPB continuum.
This theory represents the reaction field induced by the continuum
in terms of charge and dipole densities localized within the molecular system.
Because these densities cannot be calculated analytically for
systems of arbitrary shape, we introduce an atom-based discretization and
a set of carefully designed approximations. This
allows us to represent the densities by charges and dipoles located
at the atoms. Coupled systems of linear equations determine
these multipoles and can be rapidly solved
by iteration during an MD simulation. The multipoles yield
the reaction field forces and energies.
Finally, we scrutinize the quality of our approach by comparisons with
an analytical solution restricted to perfectly spherical systems
and with results of a finite difference method.
BMO authors (in alphabetic order):
Long-range electrostatics in molecular dynamics simulations