Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization

Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization

Despite considerable advances in computing power, atomistic simulations under nonperiodic boundary conditions, with Coulombic electrostatic interactions and in systems large enough to reduce finite-size associated errors in thermodynamic quantities to within the thermal energy, are still not affordable. As a result, periodic boundary conditions, systems of microscopic size and effective electro...

Electrostatic interactions in charged nanoslits within an explicit solvent theory.

Within a dipolar Poisson-Boltzmann theory including electrostatic correlations, we consider the effect of explicit solvent structure on solvent and ion partition confined to charged nanopores. We develop a relaxation scheme for the solution of this highly non-linear integro-differential equation for the electrostatic potential. The scheme is an extension of the approach previously introduced fo...

Inter-DNA electrostatics from explicit solvent molecular dynamics simulations.

Electrostatic interactions drive a compaction of many biomolecules, such as RNA and DNA.1,2 For example, DNA is compacted a million-fold into a highly organized structure in eukaryotic cells, called chromatin.2-5 Understanding the mechanism of chromatin folding is of great biological importance, since it mediates the extent of accessibility of specific DNA sequences, which in turn, controls imp...

Coarse grained potential functions for proteins derived from all-atom explicit-solvent molecular dynamics simulations

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

pH is an important parameter in condensed-phase systems, because it determines the protonation state of titratable groups and thus influences the structure, dynamics, and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fixed and cannot adapt to changes of the local environment. Here, we present ...