PyBiLayers: A Python Tool to Automate the Analysis of Membrane-Based Molecular Dynamics Simulations

Abstract

From a biological point of view, the study of lipid bilayers is of great importance as they form part of the plasmatic membrane in each and every living cell. Due to the complexity of their basic functions, the mechanical properties of lipid bilayers have long been studied. These investigations have not been limited to experimental approaches and there are now many research groups tackling the problem from a computer simulation perspective. In general, these studies are performed using classical molecular dynamics simulations with coarse grained lipids (MARTINI force field). It is the analysis of these simulations that allows for a potentially greater understanding of bilayers mechanics. In this work, we present a new tool which has been specifically designed for lipid bilayer simulations. The tool focuses on two areas 1) the analysis of the thermodynamic quantities of the system, and 2) structural analysis based on the instantaneous configurations of the system. Designed with generality at its forefront, the tool can read configurations of a given membrane and, through the incorporation of the vectorised libraries available in python, users can expect a high throughput of complex analyses on a modern desktop computer. The implementation of this tool in the wider biophysics of lipid membranes community will provide consistent, standarised results and, therefore, open a new pathway to a greater understanding of lipid bilayer mechanics.