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This is a manual for the gorder tool—a command-line (CLI) application, Python package, and Rust crate for calculating lipid order parameters from molecular simulations. Most of the manual focuses on the CLI application.

The contents of this manual are shown in the panel on the left side of the page.

In the Introduction section, we discuss why gorder exists and what lipid order parameters even are. Feel free to skip this section.

In the Beginner section, we describe how to install gorder and run basic analyses of atomistic, coarse-grained, and united-atom systems. If you are only interested in, for example, atomistic systems, you can skip the pages dedicated to coarse-grained and united-atom analyses.

In the Advanced section, we discuss various features of gorder, such as calculating order parameters for individual leaflets, constructing order parameter maps, estimating analysis errors, calculating order parameters in a specific part of the membrane, and analyzing simulations using dynamically estimated membrane normals. The individual pages are quite independent, so you can skip directly to the ones you need.

In the Expert section, we cover more advanced features of gorder, which mostly provide greater control over the analyses. This includes manual lipid assignment to leaflets, manual specification of membrane normals, and ignoring periodic boundary conditions. You will most likely not need these features.

In the APIs section, we briefly explain how to use gorder directly as a Python package or a Rust crate. These topics also have their own dedicated manuals (Python, Rust). The CLI version of gorder is fully featured; you do not need to use the APIs unless you want direct integration with your code.

In the Meta section, we discuss the limitations of gorder (you should read this page!), where to send your feedback, and how to cite gorder if you use it in a scientific project.