United-atom simulation

United-atom simulations except AA, all-atom simulations. 

Theodorou, D.N., Muller-Plathe, F., and Milano, G. (2007) Coarse-grained and reverse-mapped united-atom simulations of long-chain atactic polystyrene melts structure, thermodynamic properties, chain conformation, and entanglements. Macromolecules, 40, 3876-3885. 

Temperature also determines step size. An acceptable time step for room temperature simulations is about 0..5-1 fs for All Atom system s or for sim Illation s that do not con strain hydrogen atoms. For United Atom systems or systems containing only heavy atoms, you can use steps of 1-2 fs. 

In a united atomforce field the van der Waals centre of the united atom is usually associated v ilh the position of the heavy (i.e. non-hydrogen) atom. Thus, for a united CH3 or CH2 group the vem der Waals centre would be located at the carbon atom. It would be more accurate to associate the van der Waals centre with a position that was offset slightly from the carbon position, in order to reflect the presence of the hydrogen atoms. Toxvaerd has developed such a model that gives superior performance for alkemes than do the simple united atom models, particularly for simulations at high pressures [Toxvaerd 1990]. In... 

Force fields split naturally into two main classes all-atom force fields and united atom force fields. In the former, each atom in the system is represented explicitly by potential functions. In the latter, hydrogens attached to heavy atoms (such as carbon) are removed. In their place single united (or extended) atom potentials are used. In this type of force field a CH2 group would appear as a single spherical atom. United atom sites have the advantage of greatly reducing the number of interaction sites in the molecule, but in certain cases can seriously limit the accuracy of the force field. United atom force fields are most usually required for the most computationally expensive tasks, such as the simulation of bulk liquid crystal phases via molecular dynamics or Monte Carlo methods (see Sect. 5.1). 

Jorgensen et al. has developed a series of united atom intermolecular potential functions based on multiple Monte Carlo simulations of small molecules [10-23]. Careful optimisation of these functions has been possible by fitting to the thermodynamic properties of the materials studied. Combining these OPLS functions (Optimised Potentials for Liquid Simulation) with the AMBER intramolecular force field provides a powerful united-atom force field [24] which has been used in bulk simulations of liquid crystals [25-27],... 

MD simulations also provide an opportunity to detect the structure of molecularly thin films. The most commonly known ordering structure induced by the confinement, the layering, has been revealed that the molecules are packed layer by layer within the film and the atoms would concentrate on several discrete positions. This has been confirmed in the simulations of liquid decane [29]. The density profile of unite atoms obtained from the simulations is given in Fig. 12 where two sharp density peaks appear at the locations near the walls, as a result of adsorption, while in the middle of the film smaller but obvious peaks can be observed on the density profile. The distance between the layers is largely identical to the thickness of the linear chain of decane molecules, which manifests the layered packing of molecules. 

MD simulations of melts of C44H90, based on classic techniques in continuous space, have been reported recently using united atom [146] and fully atomistic [145] representations of the chain. Time in the conventional MD simulations is expressed in seconds, whereas time in the simulation of the coarse-grained chains on the 2nnd lattice is expressed in MC steps. Nevertheless, a few comparisons are possible via the longest relaxation time, rr, deduced from the decorrelation of the end-to-end vector ... 

Fig. 5.5. Illustration of the coarse-graining procedure for a united atom chain. The chain is a segment of PE at 509 K from molecular dynamics simulations with the united atom model [Eqs. (5.7)—(5.11)]. One coarse-grained bond represents the end-to-end distance of n = 5 consecutive united atom bonds. From [32]...

Attempts were made to include all hydrogen atoms explicitly in the simulations. This computationally demanding explicit-atom model shows (Fig. 1) that the crystal symmetry is orthorhombic, in agreement with the well-known experimental result for polyethylene single crystals, instead of the hexagonal symmetry seen in united-atom model simulations. 

However, the essential mechanisms of lamellar formation and growth are found to be the same in both the united-atom and explicit-atom models. Only the united-atom model simulation results are therefore discussed in Sect. 3. 

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