Explicit atoms

Most liquid phase molecular simulations with explicit atomic polarizabilities are performed with MD rather than MC techniques. This is due to the fact that, despite its general computational simplicity, MC with explicit polarization [173, 174] requires that Eq. (9-21) be solved every MC step, when even one molecule in the system is moved, and the number of configurations in an average Monte Carlo computation is orders of magnitude greater than in a MD simulation. For nonpolarizable, pairwise-additive models, MC methods can be efficient because only the... 

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. 

The introduction of the external potential Vex, in Equation 4 is designed to mimic the effect of the surrounding (implicit) bulk solvent on the system by restricting the movement of any explicit water molecules.49 Thus, Vex[ is interpreted as arising from the force exerted on the explicit atoms by the implicit surrounding bulk solvent. This restraining potential has the simple harmonic form,49... 

Density functional methods treat larger molecules more successfully than ab-initio methods and also make use of explicit atomic basis sets as described for ab-initio methods. 

Fig. 3.9 Dynamic structure factor for a 100 monomer PE chain in the melt at 509 K vs. scaled time for the experiment (symbols), the united atom model (full curves) and the explicit atom model (dashed curves). (Reprinted with permission from [52]. Copyright 1998 American Institute of Physics)...

The change in velocity vt is equal to the integral of acceleration over time. In MolD, one numerically and iteratively integrates the classical equations of motion for every explicit atom N in the system by marching forward in time by tiny time increments, At. A number of algorithms exist for this purpose (Brooks et al., 1988 McCammon and Harvey, 1987), and the simplest formulation is shown below ... 

Molecular dynamics simulations are attractive because they can provide not only quantitative information about rates and pathways of reactions, but also valuable insight into the details of ho y the chemistry occurs. Furthermore, a dynamical treatment is required if the statistical assumption is not valid. Yet another reason for interest in explicit atomic-level simulations of the gas-phase reactions is that they contribute to the formulation of condensed-phase models and, of course, are needed if one is to include the initial stages of the vapor-phase chemistry in the simulations of the decomposition of energetic materials. These and other motivations have lead to a lot of efforts to develop realistic atomic-level models that can be used in MD simulations of the decomposition of gas-phase energetic molecules. 

The first computational investigations of phospholipids were undertaken using purely statistical methods to describe overall properties. In the 1980s the simulation of molecules and their behavior using an explicit atomic description was extended to large systems such as proteins and lipids. To simulate the static and dynamic behav-... 

D. Y. Yoon, G. D. Smith, and T. Matsuda,/. Chem. Phys., 98,10037 (1993). A Comparison of a United Atom and an Explicit Atom Model in Simulations of Polymethylene. 

P.-O Astrand, P. Linse and G. Kalstrdm, Molecular dynamics study of water adopting a potential function with explicit atomic dipole moments and anisotropic polarizabilities, Chem. Phys., 191 (1995) 195-202. 

Hybrid models are usuaDy used to study defective surfaces. In these models the internal surfaces of a slit pore, defined by a stack of mean-field layers, are coated by one or more graphene layers with explicit atomic structure. To generate defects one or more carbon atoms are removed from one or more explicit graphene layers [19, 20]. 

Earlier work in this area of shape analysis focused on QSAR studies accounting for conformational features of molecules, such as interatomic distances [89], explicit atomic coordinate sets [90], computed intermolecular distances [91], and simpler shape descriptors such as molecular volume [92]. Each of these descriptor types formally requires conformational analysis, and therefore produces, accordingly, a family of solutions for most structures. 

Lynden-Bell and coworkers examined the validity of this approximation by simulating systems with fully explicit methyl groups (i.e. aU hydrogens) as well as united atom models. They found that the united atom approximation leads to a higher density in both the liquid and crystalline states. As a consequence, the dynamics of the united atom system are somewhat slower than for the case of the explicit atom model. 

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