Molecular dynamics simulation simple models

Abstract Theoretical investigations of ionic liquids are reviewed. Three main categories are discussed, i.e., static quantum chemical calculations (electronic structure methods), traditional molecular dynamics simulations and first-principles molecular dynamics simulations. Simple models are reviewed in brief. 

Since this behavior is universal, it is obvious that the simplest simulation models which contain the essential aspects of polymers are sufficient to study these phenomena. Two typical examples of such models are the bond fluctuation Monte Carlo model and the simple bead-spring model employed in molecular dynamics simulations. Both models are illustrated in Fig. 6. 

Juffer, A.H., Berendsen, H.J.C. Dynamic surface boundary conditions A simple boundary model for molecular dynamics simulations. Mol. Phys. 79 (1993) 623-644. 

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

Fig. 7 gives an example of such a comparison between a number of different polymer simulations and an experiment. The data contain a variety of Monte Carlo simulations employing different models, molecular dynamics simulations, as well as experimental results for polyethylene. Within the error bars this universal analysis of the diffusion constant is independent of the chemical species, be they simple computer models or real chemical materials. Thus, on this level, the simplified models are the most suitable models for investigating polymer materials. (For polymers with side branches or more complicated monomers, the situation is not that clear cut.) It also shows that the so-called entanglement length or entanglement molecular mass Mg is the universal scaling variable which allows one to compare different polymeric melts in order to interpret their viscoelastic behavior. 

For any even vaguely realistic atomically constituted membrane it is unlikely that any theory will become available in the near future which will properly or reasonably describe the dynamic properties of the membrane, the fluids near it, and their passage, or selective passage, through it. Nevertheless, one should continue trying with simple models and simple theories [39-43], which show the way forward and can, as usual, be tested by the virtually exact results of molecular dynamics simulation. 

The favourable properties which mark out vesicles as protocell models were confirmed by computer simulation (Pohorill and Wilson, 1995). These researchers studied the molecular dynamics of simple membrane/water boundary layers the bilayer surface fluctuated in time and space. The model membrane consisted of glycerine-1-monooleate defects were present which allowed ion transport to occur, whereby negative ions passed through the bilayer more easily than positive ions. The membrane-water boundary layer should be particularly suited to reactions which are accelerated by heterogeneous catalysis. Thus, the authors believe that these vesicles fulfil almost all the conditions required for the first protocells on earth ... 

The attenuation of die dipole of the repeat unit owing to thermal oscillations was modeled by treating the dipole moment as a simple harmonic oscillator tied to the motion of the repeat unit and characterized by the excitation of a single lattice mode, the mode, which describes the in-phase rotation of the repeat unit as a whole about the chain axis. This mode was shown to capture accurately the oscillatory dynamics of the net dipole moment itself, by comparison with short molecular dynamics simulations. The average amplitude is determined from the frequency of this single mode, which comes directly out of the CLD calculation ... 

O.A. Karim et al., The ice/water interface A molecular dynamics simulation using the simple point charge model. J. Chem. Phys. 92, 4634 1635 (1990)... 

We showed previously that a simple model for the ion-hydration interactions, which separates the ion-hydration forces in a long-range term due to the behavior of water as a continuous dielectric (the screened image force) and a short-range term due to the discreetness of the water molecules (SM/SB), can explain almost quantitatively a number of phenomena related to the electrolyte interfaces.6 In this article, we examined the limitations of the model in predicting the distributions of ions near the air/water interface, by comparison with molecular dynamics simulations. It is clear that the real ion-hydration forces are more complicated than the simple model employed here however, the interfacia] phenomena (including specific ionic effects) can be understood, at least qualitatively, in terms of this simple approach. 

Now that we have settled on a model, one needs to choose the appropriate algorithm. Three methods have been used to study polymers in the continuum Monte Carlo, molecular dynamics, and Brownian dynamics. Because the distance between beads is not fixed in the bead-spring model, one can use a very simple set of moves in a Monte Carlo simulation, namely choose a monomer at random and attempt to displace it a random amount in a random direction. The move is then accepted or rejected based on a Boltzmann weight. Although this method works very well for static and dynamic properties in equilibrium, it is not appropriate for studying polymers in a shear flow. This is because the method is purely stochastic and the velocity of a mer is undefined. In a molecular dynamics simulation one can follow the dynamics of each mer since one simply solves Newton s equations of motion for mer i,... 

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