Login / Signup

Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations.

Dominik SidlerSimon FraschMichael Cristòfol-CloughSereina Riniker
Published in: The Journal of chemical physics (2018)
Reaction-field (RF) methods have been extensively used in molecular dynamics simulations to efficiently compute long-range electrostatic interactions. They assume a continuous dielectric medium outside a certain cutoff, which has shown to be a reasonable approximation in many cases. However, lattice sum or fast multipole methods are nowadays often used instead, which treat long-range interactions explicitly but may introduce different artefacts. In the following work, the major issue of RFs is addressed, i.e., their inability to account for inhomogeneity even in heterogenous environments (e.g., membranes or protein binding pockets). By using a first-order Laplace series expansion of the dielectric permittivity on the cutoff sphere, local anisotropic effects can be described in a simple form. It is shown that the resulting boundary-value problem cannot be solved analytically, but instead a well-behaved approximative anisotropic reaction field (ARF) is introduced, which preserves coordinate invariance and approaches the standard RF solution for homogeneous systems. The comparison of RF to the state-of-the-art particle-particle particle-mesh (P3M) method shows a difference in the orientation of molecules close to the interface between two different dielectrics (water/chloroform). It was found that the ARF leads to a correction of the orientational distribution toward the P3M reference for planar and spherical interfaces.
Keyphrases
  • molecular dynamics simulations
  • molecular docking
  • finite element
  • binding protein
  • electron transfer
  • transcription factor
  • high temperature