Bending Lipid Bilayers
Membrane curvature regulates the structure, organization, and conformational dynamics of many membrane-embedded protein assemblies, yet all-atom molecular dynamics (MD) simulations are almost always carried out on flat membrane patches under periodic boundary conditions. This chapter gives step-by-step instructions for converting an equilibrated planar lipid bilayer into a curved, bicelle-like membrane patch of prescribed radius using grid-based external potentials in NAMD. The potential acts only on the phosphate, glycerol, and acyl-chain atoms of the lipids, so the bilayer stays intact and fluid while it is bent gradually over a series of short simulations. We describe how to configure the provided VMD, Python, and NAMD scripts, how the planar and curved confinement grids are constructed, how to run the iterative bending simulations, and how to check the result. As a worked example, we bend a patch of 686 DSPC lipids to a radius of 150 Å.