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

• DOI: 10.1021/acs.jctc.1c00447
• Publication Date: 2021-08-27T21:02:13Z
• Authors: Paul Smith; Christian D. Lorenz
• Keywords: Python; Implementation; On the fly

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 LiPyphilic include the identification of cholesterol flip-flop events, classification local environments, degree interleaflet registration. is both force field- resolution-agnostic, by using powerful atom selection language MDAnalysis, it can handle highly also offers two on-the-fly trajectory transformations (i) fix split across periodic boundaries (ii) perform nojump coordinate unwrapping. Our implementation unwrapping accounts fluctuations box volume under NPT ensemble—an issue that most current implementations have overlooked. The full documentation LiPyphilic, including installation instructions links interactive online tutorials, available at https://lipyphilic.readthedocs.io/en/latest.