Molecular dynamics , atomistic

An interesting approach has recently been chosen in the MBO(N)D program ([Moldyn 1997]). Structural elements of different size varying from individual peptide planes up to protein domains can be defined to be rigid. During an atomistic molecular dynamics simulation, all fast motion orthogonal to the lowest normal modes is removed. This allows use of ca. 20 times longer time steps than in standard simulations. 

Fig. 13 Structures resulting from atomistic molecular dynamics simulations of Pj j-2 tapes (left), ribbons (middle) and fibrils (right) viewed perpendicular to (top) and along (bottom) the long axis of the tape. Hydrogen atoms and solvent molecules are not shown for clarity...

The aim of the force matching procedure is to obtain the effective pair-force between CG sites using the force data obtained from a detailed atomistic molecular dynamics (MD) trajectory. The current implementation of the force-matching method closely follows the formulation from Refs. [23, 24],... 

The earliest fully atomistic molecular dynamic (MD) studies of a simplified Nation model using polyelectrolyte analogs showed the formation of a percolating structure of water-filled channels, which is consistent with the basic ideas of the cluster-network model of Hsu and Gierke. The first MD... 

Gurtovenko, A.A., Vattulainen, I. Pore formation coupled to ion transport through lipid membranes as induced by transmembrane ionic charge imbalance atomistic molecular dynamics study. J. Am. Chem. Soc. 2005, 127, 17570-1. 

Wohlert, J., den Otter, W.K., Edholm, O., Briels, W.J. Free energy of a trans-membrane pore calculated from atomistic molecular dynamics simulations. J. Chem. Phys. 2006, 124, 154905. 

This bimodal dynamics of hydration water is intriguing. A model based on dynamic equilibrium between quasi-bound and free water molecules on the surface of biomolecules (or self-assembly) predicts that the orientational relaxation at a macromolecular surface should indeed be biexponential, with a fast time component (few ps) nearly equal to that of the free water while the long time component is equal to the inverse of the rate of bound to free transition [4], In order to gain an in depth understanding of hydration dynamics, we have carried out detailed atomistic molecular dynamics (MD) simulation studies of water dynamics at the surface of an anionic micelle of cesium perfluorooctanoate (CsPFO), a cationic micelle of cetyl trimethy-lainmonium bromide (CTAB), and also at the surface of a small protein (enterotoxin) using classical, non-polarizable force fields. In particular we have studied the hydrogen bond lifetime dynamics, rotational and dielectric relaxation, translational diffusion and vibrational dynamics of the surface water molecules. In this article we discuss the water dynamics at the surface of CsPFO and of enterotoxin. 

Atomistic molecular dynamics simulations of one molecule of 1ETN soaked in water were performed under constant volume and temperature conditions (NVT). Details of the simulation can be found elsewhere [13]. 

Figure 5 Snapshot of a lipid raft system studied through atomistic molecular dynamics simulations (42). Water is shown at the top and at the bottom in light color, while the membrane is in the middle of the figure. In the bilayer, rigid cholesterol molecules are shown in light grey, POPC in dark grey, and sphingomyelin in intermediate grey.

Turner et al. [83] of the HI decomposition reaction, 2HI = H2 + I2, in carbon slit pores and carbon nanotubes. Large increases occurred (by up to a factor of 60) in the reaction rate, due to selective attraction of the transition state species to the pore walls. This selective attraction arises because the transition species is larger than other molecular species in the reaction mixture and has a stronger dispersion interaction with the carbon wall. More rigorous and complete calculations require the use of a dual scale approach, involving ab initio methods to determine the potential energy surface of the reaction, and atomistic molecular dynamics simulations to determine reaction rates [41]. 

Tsolou, G., Harmandaris, V.A., and Mavrantzas, V.G. (2006) Atomistic molecular dynamics simulation of the temperature and pressure dependences of local and terminal relaxations in cz5-1,4-polybutadiene, J. Chem. Phys. 124, 084906... 

In a recent work, the translational motion of 4- -hexyl-4 -cyanobiphenyl (6CB) was studied in the isotropic phase by atomistic molecular dynamics simulation [134], The mean-square displacement showed evidence of sub-diffusive dynamics, with a plateau that became very apparent at the lowest temperatures. A three-time self-intermediate scattering function revealed that this plateau was connected with a homogeneous dynamics that, at longer times, became heterogeneous and finally exponential. These features, which are shared by, for example, a high-density system of hard spheres, support the universal character of the translational dynamics of liquids in their supercooled regime. 

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