Lipid Bilayer Shearing

From: Sachin Natesh (snatesh_at_uchicago.edu)
Date: Tue Aug 16 2016 - 12:01:15 CDT

Hello,

I am simulating peptides above a lipid bilayer in the NPT ensemble. After
~200ns of production, the membrane layers appear to undergo in-plane
shearing (in the unwrapped trajectory, see links for screenshots). My
periodic boundary conditions minimize the x/y distance between images, so
the membrane is 'infinite' in the x-y plane. The only deformation is the
inter-layer shear and fragmentation at the edges of the membrane (see link
for membrane w/ multiple periodic images).

Has anyone observed this behavior for similar systems? Might this be an
artifact of unwrapping, or improper handling of image centering?

Any help is appreciated!

Thanks,
Sachin Natesh

https://www.dropbox.com/s/i1rlm0zm7zki46l/after.png?dl=0
https://www.dropbox.com/s/313ywglb0mghlzw/before.png?dl=0
https://www.dropbox.com/s/h60m05g6akt9n7z/top.png?dl=0

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