Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?

Abstract

Biological processes occur on space and time scales that are often unreachable for fully atomistic simulations. Therefore, simplified or coarse grain (CG) models for the theoretical study of these systems are frequently used. In this context, the accurate description of solvation properties remains an important and challenging field. In the present work, we report a new CG model based on the transient tetrahedral structures observed in pure water. Our representation lumps approximately 11 WATer molecules into FOUR tetrahedrally interconnected beads, hence the name WAT FOUR (WT4). Each bead carries a partial charge allowing the model to explicitly consider long-range electrostatics, generating its own dielectric permittivity and obviating the shortcomings of a uniform dielectric constant. We obtained a good representation of the aqueous environment for most biologically relevant temperature conditions in the range from 278 to 328 K. The model is applied to solvate simple CG electrolytes developed in this work (Na + , K + , and Cl -) and a recently published simplified representation of nucleic acids. In both cases, we obtained a good resemblance of experimental data and atomistic simulations. In particular, the solvation structure around DNA, partial charge neutralization by counterions, preference for sodium over potassium, and ion mediated minor groove narrowing as reported from X-ray crystallography are well reproduced by the present scheme. The set of parameters presented here opens the possibility of reaching the multimicroseconds time scale, including explicit solvation, ionic specificity, and long-range electrostatics, keeping nearly atomistic resolution with significantly reduced computational cost.

Comparative assessment of the ELBA coarse-grained model for water

“…WT4 is a model where groups of 11 water molecules are represented by 4 charged sites [103]. WT4 was employed to solvate ions and nucleic acids [103]. The model reproduces well the experimental density and the diffusion coefficient; however, the surface tension is substantially smaller than the experimental value.…”

“…The value of the surface tension, while significantly lower than the experimental value, is better than several other coarsegrained models. WT4 is a model where groups of 11 water molecules are represented by 4 charged sites [103]. WT4 was employed to solvate ions and nucleic acids [103].…”

“…Regarding the calculation of the diffusion coefficient for those models mapping more than one real water molecule to a coarse-grained site, it should be noted that two different approaches are used. Some workers multiply the diffusion coefficient of the coarse-grained water by the number of real water molecules that a coarse-grained unit represents [97,98,103]; however, others do not apply such scaling [101]. Table 7 reports the diffusion data as originally published.…”

Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk

“…22 In this contribution, we present a dual resolution model for aqueous solvation belonging to the second approach (fixed resolution). It is based on the combined use of the popular SPC water model 23 together with our recently developed CG model for water, called WatFour (WT4, for shortness 24 ). In this CG model, four linked beads are placed at the corners of a regular tetrahedron whose geometry corresponds to that of the tetrahedral structure of water ( Figure 1A).…”

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

“…The speedup of such multiscale simulations with respect to all-atom simulations is proportional to the reduction of the interaction sites in the coarse-grained (CG) model of water. Consequently, from the viewpoint of computational efficiency it is advantageous to use a supramolecular CG model [10][11][12][13], where several water molecules are represented with a single effective bead.…”