Full scale structural, mechanical and dynamical properties of HIV-1 liposomes
Fig 2
Hydrophobic thickness analysis.
A Clipped view of the carbon bead selection used for thickness calculation. The selection is superimposed with the volume grid employed to determine the leaflet in which each ‘C2B’ bead resides; blue represents the outer monolayer and green the inner monolayer. The inset shows a zoomed in view of the leaflets delineated by the volume grid, the latter yielded by measure volinterior. B The uniform point distribution (N = 1024) used to sample thickness, yielded via Poisson disk sampling. C Uniform distribution with the volume grid. The inset demonstrates the carbon beads isolated about each test point, in a search radius rsearch of 46 Å. Hydrophobic thickness is considered as the center of mass distance between groups of C2B beads in each leaflet. D Resulting analysis over the 5.2 μs trajectory. The dark line shows the mean hydrophobic thickness per frame, while the transparent region shows the standard deviation at each frame for the 1024 values calculated. The mean thickness over the time series, dotted line, is 26 Å with a standard deviation of 1 Å between frames.