Model all-atom

Fig. 1. The time evolution (top) and average cumulative difference (bottom) associated with the central dihedral angle of butane r (defined by the four carbon atoms), for trajectories differing initially in 10 , 10 , and 10 Angstoms of the Cartesian coordinates from a reference trajectory. The leap-frog/Verlet scheme at the timestep At = 1 fs is used in all cases, with an all-atom model comprised of bond-stretch, bond-angle, dihedral-angle, van der Waals, and electrostatic components, a.s specified by the AMBER force field within the INSIGHT/Discover program.

ALL-ATOM MODELS FOR PROTON TRANSFER REACTIONS IN ENZYMES... 

Proton transfer reactions, 143-144, 144 activation energy, 149,164 all-atom models for, 146-148 Cys 25-His 159 in papain, 140-143 computer program for EVB calculations, 150-151... 

All-Atom Models for Proton Transfer Reactions in Enzymes, 146... 

Mirny, L., and Shakhnovich, E. (2001). Protein folding theory From lattice to all-atom models. Annu. Rev. Biophys. Biomolec. Strud. 30, 361-396. 

The opposite approach has also been considered to make accuracy paramount, independent of computational cost. For example, these cases typically employ the most accurate methods and complex sampling methods, both of which contribute to the computational complexity of the calculation. Clearly, just because a calculation is computationally demanding does not in itself demonstrate that it will be more accurate. However, elements which contribute to the accuracy of a calculation in terms of more accurate models — e.g., all-atom models, explicit solvation — or enhancing the degree of sampling would clearly be more computationally demanding. 

Kaminski, G. Duffy, E. M. Matsui, T. Jorgensen, W. L., Free-energies of hydration and pure liquid properties of hydrocarbons from the OPLS all-atom model, J. Phys. Chem. 1994, 98, 13077-13082. 

We wish to reiterate the theme of combining implicit representations of the solvent environment with all-atom models of the biomacromolecules taking advantage of the sampling benefits of MC. Clearly, the boundaries of computer... 

In practice, empirical or semi-empirical interaction potentials are used. These potential energy functions are often parameterized as pairwise additive atom-atom interactions, i.e., Upj(ri,r2,..., r/v) = JT. u ri j), where the sum runs over all atom-atom distances. An all-atom model usually requires a substantial amount of computation. This may be reduced by estimating the electronic energy via a continuum solvation model like the Onsager reaction-field model, discussed in Section 9.1. 

Once the computational model of the molecule is created, it is of most interest to study its properties in the natural environment, in particular, water solvent. Surrounding the molecule with water, allows us to study the solvation process. Like molecules, the solvent may be also described with different levels of accuracy. Beginning with all-atom models of water,48,49 which allow for the studies of solvent structure around solutes but are time consuming and the results are model dependent, to continuous dielectric models,50- 52 which are faster but less accurate and give no knowledge about the solvent itself. Thus, the difference in the level of description for both models is either an advantage or a drawback. These models are commonly known as explicit or implicit solvent models, respectively. 

A major difficulty in creating coarse-grain models is their parameterization, which often requires detailed comparison with the results of all-atom simulations as well as experimental data. However, the advantage is not only that fewer degrees of freedom exist, but also that the energy landscape is generally smoother than in an all-atom model therefore, it is easier to optimize configurations. 

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