Membrane Curvature
This is an MDAnalysis module to calculate membrane curvature from molecular dynamics simulations.
The MDAkit for membrane curvature analysis is part of the Google Summer of Code program and it is linked to a Code of Conduct.
Abstract
Elements of differential geometry enable us to quantify the curvature of a surface. The core elements of biological membranes, phospholipids, provide tridimensional configurations from which a surface can be derived to calculate curvature descriptors. We would like to integrate to MDAnalysis an analysis module to calculate average mean and Gaussian curvature from Molecular Dynamics simulations. By integrating a membrane curvature analysis module in MDAnalysis, users will benefit from a tool that enables rapid extraction of relevant properties of lipid bilayers in biomolecular systems. Our approach extracts key elements of the membrane using phospholipid head groups to define a surface, followed by a transformation into NumPy arrays. In this way, the functionality offered by NumPy and SciPy can be used to derive values of mean and gaussian curvature of biological membranes. Since MDAnalysis already works very well to explore data interactively, visualization of the membrane curvature analysis outputs in 2D-maps can be easily performed.
Disclaimer:
Code in this repository is under active developmentand is NOT guaranteed to be bug free. Use it at your own risk.
