Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

You’ve supercharged your research process with ACS and Mendeley!

Click to create an ACS ID

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Your Mendeley pairing has expired. Please reconnect
ACS Publications. Most Trusted. Most Cited. Most Read
My Activity

Figure 1Loading Img

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
Copyright © 2021 American Chemical Society

    Article Views





    Other access options
    Supporting Info (1)»


    Abstract Image

    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

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.


    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. You can change your affiliated institution below.

    Supporting Information

    Jump To

    The Supporting Information is available free of charge at

    • 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)

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system:

    Cited By

    This article is cited by 18 publications.

    1. Charlotte Bouquiaux, Benoît Champagne, Pierre Beaujean. Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes. Journal of Chemical Information and Modeling 2024, 64 (2) , 518-531.
    2. Amit Naglekar, Amitabha Chattopadhyay, Durba Sengupta. Palmitoylation of the Glucagon-like Peptide-1 Receptor Modulates Cholesterol Interactions at the Receptor–Lipid Microenvironment. The Journal of Physical Chemistry B 2023, 127 (51) , 11000-11010.
    3. Kai Steffen Stroh, Paulo C. T. Souza, Luca Monticelli, Herre Jelger Risselada. CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization. Journal of Chemical Theory and Computation 2023, 19 (22) , 8384-8400.
    4. Markéta Paloncýová, Martin Šrejber, Petra Čechová, Petra Kührová, Filip Zaoral, Michal Otyepka. Atomistic Insights into Organization of RNA-Loaded Lipid Nanoparticles. The Journal of Physical Chemistry B 2023, 127 (5) , 1158-1166.
    5. Denys E. S. Santos, Kaline Coutinho, Thereza A. Soares. Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape. Journal of Chemical Information and Modeling 2022, 62 (19) , 4690-4701.
    6. Bradley S. Harris, Yuqi Huang, Arpad Karsai, Wan-Chih Su, Pallavi D. Sambre, Atul N. Parikh, Gang-yu Liu, Roland Faller. Impact of Surface Polarity on Lipid Assembly under Spatial Confinement. Langmuir 2022, 38 (24) , 7545-7557.
    7. Wanling Song, Robin A. Corey, T. Bertie Ansell, C. Keith Cassidy, Michael R. Horrell, Anna L. Duncan, Phillip J. Stansfeld, Mark S. P. Sansom. PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 2022, 18 (2) , 1188-1201.
    8. J. Karl Spinti, Fernando Neiva Nunes, Manuel N. Melo. Room for improvement in the initial martini 3 parameterization of peptide interactions. Chemical Physics Letters 2023, 819 , 140436.
    9. Themistoklis Venianakis, Michael Siskos, George Papamokos, Ioannis P. Gerothanassis. NMR and DFT studies of monounsaturated and ω-3 polyunsaturated free fatty acids in the liquid state reveal a novel atomistic structural model of DHA. Journal of Molecular Liquids 2023, 376 , 121459.
    10. Nely Rodríguez-Moraga, Francisco Ramos-Martín, Sébastien Buchoux, Sonia Rippa, Nicola D’Amelio, Catherine Sarazin. The effect of rhamnolipids on fungal membrane models as described by their interactions with phospholipids and sterols: An in silico study. Frontiers in Chemistry 2023, 11
    11. Tong Lou, Xiuqin Bai, Xiaoyan He, Wencheng Liu, Zongcheng Yang, Ying Yang, Chengqing Yuan. Enhanced antifouling properties of marine antimicrobial peptides by PEGylation. Frontiers in Bioengineering and Biotechnology 2023, 11
    12. Marta Moreno, Ricardo Vilaça, Pedro G. Ferreira. Scalable transcriptomics analysis with Dask: applications in data science and machine learning. BMC Bioinformatics 2022, 23 (1)
    13. Nathan Bernhardt, José D. Faraldo-Gómez. MOSAICS: A software suite for analysis of membrane structure and dynamics in simulated trajectories. Biophysical Journal 2022, 30
    14. Natasha H. Rhys, David J. Barlow, M. Jayne Lawrence, Christian D. Lorenz. On the interactions of diols and DMPC monolayers. Journal of Molecular Liquids 2022, 364 , 119963.
    15. Bob-Dan Lechner, Paul Smith, Beth McGill, Skye Marshall, Jemma L. Trick, Andrei P. Chumakov, Charles Peter Winlove, Oleg V. Konovalov, Christian D. Lorenz, Peter G. Petrov. The Effects of Cholesterol Oxidation on Erythrocyte Plasma Membranes: A Monolayer Study. Membranes 2022, 12 (9) , 828.
    16. Andreas Haahr Larsen. Molecular Dynamics Simulations of Curved Lipid Membranes. International Journal of Molecular Sciences 2022, 23 (15) , 8098.
    17. Andreas H. Larsen, Laura H. John, Mark S.P. Sansom, Robin A. Corey. Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?. Bioscience Reports 2022, 42 (4)
    18. Simone Scrima, Matteo Tiberti, Alessia Campo, Elisabeth Corcelle-Termeau, Delphine Judith, Mads Møller Foged, Knut Kristoffer Bundgaard Clemmensen, Sharon A. Tooze, Marja Jäättelä, Kenji Maeda, Matteo Lambrughi, Elena Papaleo. Unraveling membrane properties at the organelle-level with LipidDyn. Computational and Structural Biotechnology Journal 2022, 20 , 3604-3614.