LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations

Molecular dynamics simulations are now widely used to study emergent phenomena in lipid membranes with complex compositions. Here, we present LiPyphilic.a fast, fully tested, and easy-to-install Python package for analyzing such simulations. Analysis tools in LiPyphilic include the identification of cholesterol flipflop events, the classification of local lipid environments, and the degree of interleaflet registration. LiPyphilic is both force field- and resolution-agnostic, and by using the powerful atom selection language of MDAnalysis, it can handle membranes with highly complex compositions. LiPyphilic also offers two on-the-fly trajectory transformations to (i) fix membranes split across periodic boundaries and (ii) perform nojump coordinate unwrapping. Our implementation of nojump unwrapping accounts for fluctuations in the box volume under the NPT ensemble.an issue that most current implementations have overlooked.

Automated summary

LiPyphilic is a fast, fully tested, and easy-to-install Python package for analyzing emergent phenomena in lipid membranes through molecular dynamics simulations. It offers various analysis tools and on-the-fly trajectory transformations to handle membranes with complex compositions effectively. Additionally, LiPyphilic addresses the issue of fluctuations in box volume under the NPT ensemble, which has been overlooked in most current implementations.