Bond orientational correlations distribution function

A comparison has been made of rotational isomeric state chains modelled by matrix multiplication methods, as in most of the papers mentioned in this section, with lattice and off-lattice chains obtained by Monte Carlo techniques. excluded volume effects than or Rotational angle flexibility has been expressed in the co-ordinates transform motion matrix, and its influence examined upon , the distribution function for r, and the correlation of the relative orientation of the end bonds of the polymer. ... 

Among the various types of local motions that take place in polymer liquids, the change in the orientation of individual bonds with time is one that can be readily evaluated from the molecular dynamics simulations. The bond reorientation motions are also amenaUe to experimental measurement by means of a number of techniques. We investigate the bond reorientation dynamics by evaluating three types of quantities, the distribution W(0,t) of reorientation angle 6 that a bond has undergone during a time interval t, and the time correlation functions... 

An important aspect of simulations of lipid bilayers systems is the timescale on which different motions occur. The fastest motions are small local rearrangements around bonds and the motion of water molecules (picoseconds to tens of picoseconds). Rotational correlation times for tail dihedrals are of the order of tens to hundreds of picoseconds (see Time Correlation Functions). The dihedral rotational correlation times for certain dihedrals in the headgroup is of the order of hundreds of picoseconds. Important motions like the rotation and lateral diffusion of entire lipids occur on a nanosecond scale and it is therefore not possible to sample these motions adequately within the 0.5-2 ns simulations that are usual in the current practice. This is an important consideration in creating a starting structure for a simulation. Although the precise distribution of tail dihedrals will equilibrate reasonably fast, there will remain a strong correlation of the orientation of entire lipids with the starting structure in simulations of less than several nanoseconds. 

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