I made this movie of a water molecule (red sphere) permeating a lipid bilayer. The bilayer is represented in blue sticks, and it’s hydrated by water molecules on top and bottom (red and white lines). The gray spheres are the carbon atoms of the lipid molecules. The yellow spheres are the water molecules within 10 Angstroms of the permeating water.
The frames for this movie were taken from several different simulations (since it’s hard to simulate full membrane permeation in one go). My goal in creating the movie was to see (1) that the membrane gets slightly deformed when the water molecule enters, and (2) that the water molecule that enters brings in a few of its buddies. Research is exciting sometimes!
The script I wrote to concatenate frames and wrap in the XY directions is located in my Github repo.