LiPyphilic: A Python toolkit for the analysis of lipid membrane simulations

Research output: Contribution to journalArticlepeer-review

44 Citations (Scopus)
352 Downloads (Pure)

Abstract

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 flip-flop 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. The full documentation of LiPyphilic, including installation instructions and links to interactive online tutorials, is available at https://lipyphilic.readthedocs.io/en/latest.

Original languageEnglish
Pages (from-to)5907-5919
Number of pages13
JournalJournal of Chemical Theory and Computation
Volume17
Issue number9
Early online date27 Aug 2021
DOIs
Publication statusPublished - 14 Sept 2021

Fingerprint

Dive into the research topics of 'LiPyphilic: A Python toolkit for the analysis of lipid membrane simulations'. Together they form a unique fingerprint.

Cite this