Fully atomistic methods

In simple single-site liquid crystal models, such as hard-ellipsoids or the Gay-Berne potential, a number of elegant techniques have been devised to calculate key bulk properties which are useful for display applications. These include elastic constants for nematic systems [87, 88]. However, these techniques are dependent on large systems and long runs, and (at the present time) limitations in computer time prevent the extension of these methods to fully atomistic models. 

One of the important limitations of these methods, in their current state of development, is the necessity to conduct a new coarse-graining for each new type of polymer that is simulated. Major opportunities to increase the utility of this class of simulations lie in the development of methods, which make the mapping to the coarse-grained structure (and the reverse-mapping back to the structure expressed in fully atomistic detail) as general (and painless) as possible when new polymers are treated. This area is the subject of continuing work by all four groups. 

Another methodological approach, which has become more attractive in the last few years for estimating binding free energies of protein-protein complexes, is the MM-PBSA method (Molecular Mechanics/Poisson-Boltzmann Surface Area). This method is a fully atomistic approach that combines molecular mechanics and continuum solvent, and has several appealing features as the possibility of being applied to a variety of systems not suitable for FEP such as very large protein-protein complexes.69,129-137... 

CG residues and three atomistic, and so on. In addition, they also increased the temperature of each replica, such that while the fully atomistic model was simulated at 298 K, the fully CG model was simulated at 700 K. However, despite the small size of the system, the small difference between the CG and atomistic models (OPLSUA Vi. OPLSAA) and the use of incremental coarsening, the acceptance ratio of the swap moves was still very low, running between 2.5% and 5.8%. Applications of this method to larger systems, or using a greater difference between the atomistic and CG models therefore looks problematic. 

The best (albeit rather laborious) existing method to study packing in the crystalline phase of a polymer and predict pc relatively accurately is to use fully atomistic simulations. A major... 

This chapter will review the generation of free-standing thin films and fibers with a coarse-grained simulation method on a high coordination lattice,performed in a manner that allows accurate reverse-mapping of individual replicas to a fully atomistic representation in continuous space.4 After describing some of the properties of these films and fibers, we will present some new information about the limits on the stability of the models of these nanofibers. 

When chromophores are covalently coupled in super/supramolecular objects (such as multichromo-phore-containing dendrimers), Monte Carlo-molecular dynamic calculations must be modified to take into account the restrictions on motion associated with covalent bond potentials. To accurately account for covalent bond potentials, atomistic Monte Carlo methods are required [68]. However because of the large number of atoms involved, fully atomistic calculations would be prohibitively time-consuming... 

Fully atomistic simulations are the most realistic of the three simulation methods. They include a fully detailed description of the amino acids comprising the protein, and they are thus much more true to life than the other models. In addition, solvent molecules may be added explicitly or implicitly to the simulation. Because of this extreme detail, a simulation of a small protein may require the treatment of thousands of atoms. Fully atomic simulations are thus extremely computationally expensive, and only short time scales can be explored. As computational power continues to increase, so do the time scales accessible with this method. Nevertheless, fully atomic simulations still cannot capture kinetic information they are, however, useful in understanding important local interactions that drive protein folding. 

Matching Conditions in the Quasicontinuum Method Removal of the Error Introduced at the Interface between the Coarse-Grained and Fully Atomistic... 

For fully atomistic aU-atom models, it is often difficult to find efficient MC moves to relax their configurations, and then MD is normally the method of choice. We note, however, that for chemically realistic models of polymer blends equilibration by MD methods is extremely difficult, if at all possible. Dealing with such systems is still an unsolved challenge. 

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