VMD-L Mailing List
From: Sachin Natesh (snatesh_at_uchicago.edu)
Date: Tue Aug 16 2016 - 12:01:15 CDT
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!