Why membrane structure generating?
The increase in the computational power over the past few years has allowed for all-atom molecular dynamics (MD) modeling of large biological molecules. Many of these molecules are membrane proteins, which function may (and often does) critically depend on the structure of the surrounding lipid membrane. The membrane plugin implements a simple, yet efficient, algorithm to instantly generate biological membrane structures for all-atom MD simulations of membrane proteins. Generating algorithm. The membrane plugin builds a rectangular matrix of the required size out of pre-built membrane square patches. Since biological membranes are lipid bilayers, the patches included two lipid layers, either layer being a 2-dimensional hexagonal lattice of lipids. The lipid tails were (almost) fully extended, allowing for easy inserting proteins (most of which have nearly cylindric shape) into the membrane and, therefore, reducing the required equilibration time. The distance between the layers was set
