A mean field approach for molecular simulations of fluid systems

In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

Section: Choice Of Boundary Conditionsmentioning

confidence: 99%

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

Lin

Baumketner

Deng

et al. 2009

“…1 For certain problems, however, there are good reasons to employ nonperiodic boundary conditions. [2][3][4][5][6][7][8] First, PBC can be unnecessarily costly. They require a simulation box whose shape is space-filling when periodically replicated, for example, a cube.…”

Section: Introductionmentioning

confidence: 99%

Nonperiodic stochastic boundary conditions for molecular dynamics simulations of materials embedded into a continuum mechanics domain

Rahimi

Karimi–Varzaneh

Böhm

et al. 2011

A scheme is described for performing molecular dynamics simulations on polymers under nonperiodic, stochastic boundary conditions. It has been designed to allow later the embedding of a particle domain treated by molecular dynamics into a continuum environment treated by finite elements. It combines, in the boundary region, harmonically restrained particles to confine the system with dissipative particle dynamics to dissipate energy and to thermostat the simulation. The equilibrium position of the tethered particles, the so-called anchor points, are well suited for transmitting deformations, forces and force derivatives between the particle and continuum domains. In the present work the particle scheme is tested by comparing results for coarse-grained polystyrene melts under nonperiodic and regular periodic boundary conditions. Excellent agreement is found for thermodynamic, structural, and dynamic properties.

“…Note that this corresponds to simplifying the total PMF to a single-body term, a common approximation for simple implicit solvent models. 51,53,62,63 For this study on spherical systems, these forces must be spherically symmetric. Equation (30) then calculates a radial mean force that is used to produce the optimal parameter set for the implicit solvent model.…”

Section: E Mean Force Analysismentioning

confidence: 99%

“…Even with large explicit regions, the presence of unrealistic solvent configurations is troubling, especially under consideration of the significance of long-ranged solvent mediation that occurs in confined systems. [64][65][66] Significant efforts have been directed at alleviating this problem with effective potentials 45,51,53,57,59,[61][62][63] that reproduce forces from the bulk region as faithfully as possible. While these methods have demonstrated considerable success, the full removal of boundary artifacts is not expected unless the solvent PMF is accurate within a very small tolerance.…”

Section: Introductionmentioning

confidence: 99%

“…This hybrid solvation both reduces computational expense and removes the artifacts that may arise from the use of periodic simulations. 44 A number of such hybrid models have been previously developed, 23,24,[45][46][47][48][49][50][51][52][53][54][55][56][57][58][59][60][61][62][63] many of which take advantage of particularly efficient implicit solvent models for the simple geometries of the defined explicit regions. 45,46,54,55 Hybrid solvent models are subject to artifacts due to the inability of simple continuum methods to accurately reproduce the bulk solvent PMF near the explicit/implicit boundary.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A smoothly decoupled particle interface: New methods for coupling explicit and implicit solvent

Wagoner

Pande

2011

A common theme of studies using molecular simulation is a necessary compromise between computational efficiency and resolution of the forcefield that is used. Significant efforts have been directed at combining multiple levels of granularity within a single simulation in order to maintain the efficiency of coarse-grained models, while using finer resolution in regions where such details are expected to play an important role. A specific example of this paradigm is the development of hybrid solvent models, which explicitly sample the solvent degrees of freedom within a specified domain while utilizing a continuum description elsewhere. Unfortunately, these models are complicated by the presence of structural artifacts at or near the explicit/implicit boundary. The presence of these artifacts significantly complicates the use of such models, both undermining the accuracy obtained and necessitating the parameterization of effective potentials to counteract the artificial interactions. In this work, we introduce a novel hybrid solvent model that employs a smoothly decoupled particle interface (SDPI), a switching region that gradually transitions from fully interacting particles to a continuum solvent. The resulting SDPI model allows for the use of an implicit solvent model based on a simple theory that needs to only reproduce the behavior of bulk solvent rather than the more complex features of local interactions. In this study, the SDPI model is tested on spherical hybrid domains using a coarse-grained representation of water that includes only Lennard-Jones interactions. The results demonstrate that this model is capable of reproducing solvent configurations absent of boundary artifacts, as if they were taken from full explicit simulations.