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. Author manuscript; available in PMC: 2018 Apr 20.
Published in final edited form as: J Phys Chem B. 2017 Jan 26;121(15):3424–3436. doi: 10.1021/acs.jpcb.6b09007

Figure 6.

Figure 6

Top: Normalized distribution of the helix tilt of αLAX(16) with respect to the membrane normal obtained from MD simulation of the peptide embedded into bilayer composed of DMPC and cholesterol (solid line) and DMPC and 6-ketocholestanol (dashed line) at concentrations of 10 mol% (black), 20 mol% (blue) and 40 mol% (red). Bottom: Ergodic measure calculations as a function of time. We illustrate that the standard deviation of the averaged tilt angle divided by the average of the tilt angle is proportional to N1/2 . This observation suggests that the average does not drift and is consistent with uniform sampling from the normal distribution (or Central Limit Theorem). Here the vector connecting histidine 1 and histidine 31 defines the orientation of the helix. Very similar results were obtained when all the alpha carbons of the helix were considered and the helix was overlapped with the initial configuration to determine the tilt angle. See text for more details. We have used this measure in the past for membrane simulations.72