A molecular dynamics implementation of the 3D Mercedes-Benz water model

Hynninen, Teemu; Dias, Cristiano L.; Mkrtchyan, Anna F.; Heinonen, Vili; Karttunen, Mikko; Foster, Adam S.; Ala-Nissilä, Tapio

doi:10.1016/j.cpc.2011.09.008

Cited by 12 publications

(6 citation statements)

References 29 publications

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“…Also the conviction that only explicit solvent models can describe the heat and cold denaturation naturally from first principles [31] does not seem to so self-evident as it would appear from the example of e.g. the popular Mercedes-Benz (MB) model of water [32][33][34][35]. In fact our model of a solvent with H-bonding interactions is conceptually very close to the explicit water models with directional interactions, like the MB model.…”

Section: Discussionmentioning

confidence: 84%

Unified description of solvent effects in the helix-coil transition

et al. 2014

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We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer hydrogen bonds that can compete with the intrinsic intra-polymer hydrogen bonded configurations (competing interactions) and implicit solvent action, where the solvent-polymer interactions tune biopolymer configurations by changing the activity of the solvent (non-competing interactions). The overall spin Hamiltonian is comprised of three terms: the background in vacuo Hamiltonian of the "Generalized Model of Polypeptide Chain" type and two additive terms that account for the two above mechanisms of solvent action. We show that on this level the solvent degrees of freedom can be explicitly and exactly traced over, the ensuing effective partition function combining all the solvent effects in a unified framework. In this way we are able to address helix-coil transitions for polypeptides, proteins, and DNA, with different buffers and different external constraints. Our spin-based effective Hamiltonian is applicable for treatment of such diverse phenomena as cold denaturation, effects of osmotic pressure on the cold and warm denaturation, complicated temperature dependence of the hydrophobic effect as well as providing a conceptual base for understanding the behavior of intrinsically disordered proteins and their analogues.

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Section: Discussionmentioning

confidence: 84%

Unified description of solvent effects in the helix-coil transition

et al. 2014

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“…The two mechanisms are reflected in the free energy of transfer per unit solute surface area that, when plotted as a function of a solute size, scales differently for small and large solutes. 27 It is worth mentioning that recently Dias et al 25,26,28 came up with the modified version of a 3D MB model, which includes the additional parameters and where the interaction potential depends on its local environment. With these modifications they reproduced the solid phase (ice) and pair distribution functions of real water.…”

Section: D Mb Water Modelmentioning

confidence: 99%

The application of the thermodynamic perturbation theory to study the hydrophobic hydration

Mohorič

Urbič

Hribar-Lee

2013

The Journal of Chemical Physics

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The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An excellent agreement was obtained between the theoretical and simulation results. Further, the thermodynamic perturbation theory qualitatively correctly (with respect to the experimental data) describes the solvation thermodynamics under conditions where the simulation results are difficult to obtain with good enough accuracy, e.g., at high pressures.

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“…These have been already established by Hynninen for the Mercedes-Benz water model. 46 For their integration we used a simple velocity Verlet algorithm with a time step ∆t = 10 −4 . By separately solving the equations for translational and rotational motion, we were able to set different values for the translational and rotational temperature.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Effects of translational and rotational degrees of freedom on properties of the Mercedes–Benz water model

Urbič

Mohorič

2017

The Journal of Chemical Physics

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Non-equilibrium Monte Carlo and molecular dynamics simulations are used to study the effect of translational and rotational degrees of freedom on the structural and thermodynamic properties of the simple Mercedes-Benz water model. We establish a non-equilibrium steady state where rotational and translational temperatures can be tuned. We separately show that Monte Carlo simulations can be used to study non-equilibrium properties if sampling is performed correctly. By holding one of the temperatures constant and varying the other one, we investigate the effect of faster motion in the corresponding degrees of freedom on the properties of the simple water model. In particular, the situation where the rotational temperature exceeded the translational one is mimicking the effects of microwaves on the water model. A decrease of rotational temperature leads to the higher structural order while an increase causes the structure to be more Lennard-Jones fluid like.

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A molecular dynamics implementation of the 3D Mercedes-Benz water model

Cited by 12 publications

References 29 publications

Unified description of solvent effects in the helix-coil transition

Unified description of solvent effects in the helix-coil transition

The application of the thermodynamic perturbation theory to study the hydrophobic hydration

Effects of translational and rotational degrees of freedom on properties of the Mercedes–Benz water model

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