PackMem: a versatile tool to compute and visualize interfacial packing defects in lipid bilayers

The analysis of the structural organization of lipid bilayers is generally performed across the direction normal to the bilayer/water interface, while the surface properties of the bilayer at the interface with water are often neglected. Here we present PackMem, a bioinformatic tool that performs a topographic analysis of the bilayer surface from various molecular dynamics simulations. PackMem unifies and rationalizes previous analysis based on a Cartesian grid. The grid allows identifying surface regions defined as lipid-packing defects where lipids are loosely packed, leading to cavities where aliphatic carbons are exposed to the solvent either deep or close to the membrane surface.

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