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Simulation Best Practices for Lipid Membranes

Best Practices document to be submitted to the Living Journal of Computational Molecular Science

This repository contains a document and supporting materials to lay out best practices in the modeling and molecular dynamics simulation of realistic lipid bilayer membranes, from initial model selection to rigorous property validation. Despite the seemingly specialized topic, there are a multitude of concepts and methodologies. Here, we attempt to strike a balance between completeness and prioritization. The document is intended to build theoretically- and experimentally-motivated models and simulations from the ground up; address and overcome common pitfalls; ensure accuracy, efficiency, and robustness; and ultimately bridge or at least narrow the gap between first-time simulators and world experts. For where we do not go, we provide extensive yet carefully-selected references to guide the reader in the right theoretical and practical directions.

List of Authors

-David J. Smith, University of California, Santa Barbara, Santa Barbara, CA, USA

-Jeffery B. Klauda, University of Maryland, College Park, MD, USA

-Alexander J. Sodt, National Institutes of Health, Bethesda, MD, USA

List of Contributors

-Alan M. Grossfield, University of Rochester Medical Center, Rochester, NY, USA

-O. H. Samuli Ollila, University of Helsinki and Czech Academy of Sciences

Contributing to the effort

This document is intended to be a guide that strikes a balance between completeness and prioritization. Think of this as a "quick-start" guide to express key concepts, with references to other sources for further information. If you would like to work on a section, please put your name in comments near the section or subsection title. You are welcome to work on latex "subfiles" or directly in the main document ("membranes_good.tex"). As discussed below, all contributions will be reviewed through pull requests, as well as sign-off from authors before submission.

Paper writing as code development

This paper is being developed as a living document, open to changes from the community. You can read more about the concept of writing a paper in the same way one would write software code in the essay "Paper writing as code development". If you have comments or suggestions, we welcome them! Please submit them as issues to this GitHub repository so they can be recorded and given credit for the contribution. Specific changes can be proposed via pull requests.

List of Released Versions

-v0.1: Added comprehensive content for the first draft of the document.

-v1.0: Further refinement/wordsmithing; extensive sectioning, subsectioning, and subsubsectioning; brushing up of checklist and tables; and establishment of all links to references, sections/subsections/subsubsections, tables, and other best practices documents.


-7 Jan 2019: Uploaded Published Version (1.0)

-21 Dec 2018: Uploaded ASAP Version (1.0)

-23 Nov 2018: Further updates in response to reviewer and editorial feedback.

-14 Sep 2018: Extensive updates in response to official reviewer feedback, including improved/streamlined text and additional tables, figures, and references.

-5-10 May 2018: Incorporated comments and edits from JBK and AJS, including elaboration/clarification on some practical and theoretical concepts and reference additions/updates.

-26 Mar 2018: Refined document further; established efficient sections, subsections, and subsubsections; completed all links to references, sections/subsections/subsubsections, tables, and other best practices documents.

-12 Jan 2018: Added significant amount of detail to all components of document; added a host of variables and equations, as well as images, tables, and references; reformatted contents to fit LiveCoMS Best Practices document format in LaTeX.

-Sep 2017: Added initial collection of content to GitHub via README page here.

-Aug/Sep 2017: Branched off from Interfacial Systems Best Practices Document in Google Docs (for liquid-liquid and solid-liquid interfaces) and created self-contained document for lipid bilayer membranes.


Best Practices document to be submitted to the Living Journal of Computational Molecular Science







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