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

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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
Accepted/In press10 Aug 2021
E-pub ahead of print27 Aug 2021
Published14 Sep 2021

Bibliographical note

Funding Information: Via our membership of the UK’s HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202/1, EP/R029431/1, EP/T022213), this work used the ARCHER UK National Supercomputing Service ( http://www.archer.ac.uk ) and the UK Materials and Molecular Modelling Hub (MMM Hub) for computational resources, which is partially funded by EPSRC (EP/P020194/1, EP/T022213), to carry out the MD simulations of DPPC/DOPC/Cholesterol reported in this manuscript. P.S. acknowledges the funding provided by the EPSRC DTP Studentship Block Grant (EP/N509498/1). C.D.L. acknowledges the supportive research environment of the EPSRC center for Doctoral Training in Cross-Disciplinary Approaches to Non-Equilibrium Systems (CANES, no. EP/L015854/1). Publisher Copyright: © 2021 American Chemical Society

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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.

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