On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase

Abstract

Methodology to compute the relative static dielectric permittivity and dielectric relaxation time of molecular liquids is reviewed and explicit formulas are given for the external field method in the case of simulations using a spherical cutoff, in which the background dielectric permittivity (εcs) can be larger than one, in combination with a Poisson-Boltzmann reaction-field approximation for long-range electrostatic interactions. The external field method is simple to implement and computationally efficient. It is particularly suitable for polarizable molecular models with zero permanent dipole moment and for coarse-grained molecular models with εcs > 1. The dielectric permittivities and relaxation times of water (H2O), dimethylsulfoxide (DMSO), methanol (MeOH), and chloroform (CHCl3), which range from 2 to 80 and from 5 ps to 50 ps, respectively, were calculated as an illustration.

New functionalities in the GROMOS biomolecular simulation software

“…If the COS model is used with a reaction-field, a reaction-field correction term [11] is to be added to…”

“…(19) because they contribute to the reaction-field. [11] The last term in eq. (19) is a constant that is added to represent the self-interaction of the permanent, that is, non-COS, charges.…”

“…(20). The total nonbonded potential energy is obtained by summing over all ordered pairs (i, j), thereby taking into account the different nearest neighbor and cut-off radius exclusions, [11] …”

“…The application of an external electric field enables a simple and fast way to probe the static dielectric properties of a system like the dielectric permittivity ε(0) or the Debye relaxation time τ D . [11] If a constant homogeneous external field E ext is applied to a system, for examples along the z-axis,…”

“…Here, we briefly describe some of the new functionalities that have been added since 2005: electronic polarizability, [6,7] an implicit surface area and internal volume solvation term [8] for the calculation of interatomic forces, functions required to use the GROMOS coarse-grained (CG) supramolecular force field, [9] a multiplicative switching function for nonbonded interactions, which replaces the one described in Ref. 5, adiabatic decoupling as a means to enhance the sampling of a not too large subset of degrees of freedom of a system, [10] and nonequilibrium molecular dynamics (MD) methodology to compute the dielectric permittivity and relaxation [11] or viscosity. The architecture and implementation of the GROMOS C++ code is described elsewhere, [12] as are features with regard to biomolecular structure refinement based on experimental NMR or X-ray data, [13] to the computation of relative free energies, [14] and the analysis of MD trajectories using GROMOS.…”