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

Cite this: J. Chem. Theory Comput. 2021, 17, 9, 5907–5919
Publication Date (Web):August 27, 2021
https://doi.org/10.1021/acs.jctc.1c00447
Copyright © 2021 American Chemical Society

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    Abstract

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    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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    • Comparison of LiPyphilic with other software for lipid membrane analysis; Python script for calculating the lipid enrichment index based on tail saturation; and discussion of practical issues with nojump trajectory unwrapping (PDF)

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