All-atom simulation

With all-atom simulations the locations of the hydrogen atoms are known and so the order parameters can be calculated directly. Another structural property of interest is the ratio of trans conformations to gauche conformations for the CH2—CH2 bonds in the hydrocarbon tail. The trans gauche ratio can be estimated using a variety of experimental techniques such as Raman, infrared and NMR spectroscopy. 

All-atom Simulations of Protein Unfolding and Short Peptide Folding... 

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. 

Recent computational studies of thermophilic adaptation described in this article make use of genomic/proteomic data (32, 43, 53, 62), simulations of model lattice proteins (62), and off-lattice all-atom simulations of natural proteins (43, 53). High-throughput analysis reveals signals of novel mechanisms of protein [entropic mechanism (53)] and DNA [purine-purine base stacking (32)] thermostability and urges us to consider... 

Since the experimentally determined osmotic coefficient appears to be smaller even than the molecular dynamics results, this indicates effects to be relevant that go beyond the model used for simulation. Most obvious candidates for this are the neglect of additional chemical interactions between the ions and the polyelectrolyte as well as solvation effects, i.e., interactions between the ions or the polyelectrolyte with the water molecules from the solution. It is for instance demonstrated in Ref. 46 that the osmotic coefficient also depends on whether one uses chlorine or iodine counterions. While one could certainly account for the different radii of these ions when computing the distance of closest approach entering the PB equation, the implications of the different hydration energies is much less obvious to incorporate and in principle requires very expensive all-atom simulations. 

In 2013, all-atom simulations performed on the University of Illinois massive Blue Waters computer system unlocked the detailed structure of the HIV-1 virus... 

However, there can be limits to this approach because it is not always clear whether the chosen CG mapping scheme can converge to an optimal fit. For liquid mixtures or solutions, the situation is more complex because several RDFs that mutually affect each other need to be simultaneously reproduced. In additicni, for dilute solutions, where we have a low concentration of solute, the solute-solute RDFs converge very slowly in the CG simulations. In this case, the PMF between the solute molecules can be obtained using free-energy calculation methods such as umbrella sampling or constraint dynamics. Recently, these methods have been used in an iterative optimization approach to study self-assembling dipeptides at the CG scale [75, 76]. The PMF between solute molecules in a solvent box, Fpi (r), is calculated by all-atom simulation from n distance constraint simulations ... 

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