Coarse‐grained models of water

Overview

Leonardo Darré, Matías R. Machado, Sergio Pantano

Published Online: Jun 06 2012

DOI: 10.1002/wcms.1097

Full article on Wiley Online Library: HTML PDF

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Abstract Coarse‐grained (CG) models for macromolecules have become a standard in the study of biological systems, overcoming limitations in size and time scales encountered by atomistic molecular dynamics simulations. Just as in any biomolecular ensemble, water in CG models plays a key role in mediating intermolecular and intramolecular interactions. However, owing to the highly nontrivial properties of water, important simplifications have been commonly used to treat solvation effects. Recent developments of CG models for water are overviewed, comparing some characteristic features and limitations. This article is categorized under: Molecular and Statistical Mechanics > Free Energy Methods

Explicit solvation of biomolecules. Three different explicit solvation types. (a) Atomistic double‐stranded DNA solvated within a water box. The system contains nearly 1000 and 9000 atoms of solute and solvent, respectively. (b) Equivalent system at the coarse‐grained (CG) level. The CG DNA is represented according to the model of Dans et al.,12 solvated with the Wat Four water model (see text). The system contains approximately 200 and 800 CG beads of solute and solvent, respectively. (c) Hybrid FG/CG model according to Machado et al 14 solvated with FG and CG water. This system is composed by about 1000 FG atoms and 1000 CG beads.

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Dual‐resolution simulation of water. Top, snapshot taken after 10 nanosecond of a molecular dynamic simulation of a system composed by two apposed slabs containing 2002 SPC and 368 WT4 molecules. Atomistic solvent is shown as red/white (oxygen/hydrogen). Coarse‐grained solvent is shown as light blue sticks. Bottom, mass density across an axis perpendicular to the solvents' slabs averaged over the simulation time.

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Comparison of characteristic water properties. Density (a), self‐diffusion coefficient (b), surface tension (C), and relative dielectric permittivity (D) of water are presented. Comparison is made between experimental data (black) at 29850 and the water models SPC (red),51 TIP3P (green),52,53 MARTINIp (blue),35 GROMOS (light blue),36 BMW (pink, no data reported for the self‐diffusion coefficient)37 and WT4 (yellow).38

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CG models of explicit water. (a) MARTINI model, typical van der Waals‐like model as those described by He et al. 32 (b) Three‐dimensional Mercedes–Benz model.33 The green arrows represent vectors mimicking hydrogen‐bond interactions. (c) Polarizable coarse‐grained solvent model.34 The yellow arrow represents the dipole moment. (d) MARTINIp water model.35 (e) GROMOS water model.36 (f) Big multipole water.37 (g) Wat Four model.38 The colors of the spheres refer to the charge of each bead. Blue, red, and gray correspond to positive (p), negative (q), and neutral (n), respectively. The size of the semitransparent spheres is drawn according to the Lennard–Jones radius of each model. Bond and angle parameters (r_b, k_b, θ, k_θ) are indicated.

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