gorder: Everything you will ever need for lipid order calculations

Command line tool for calculating atomistic or coarse-grained lipid order parameters from Gromacs simulations.

Installation

Install Rust
Install gorder:

$ cargo install gorder

Usage

Prepare a yaml file describing the parameters of your analysis. It's as simple as:

structure: system.tpr
trajectory: md.xtc
analysis_type: !AAOrder
    heavy_atoms: "@membrane and element name carbon"
    hydrogens: "@membrane and element name hydrogen"
output: order.yaml

Run the gorder tool. The program will automatically find bonds between the selected atoms, classify lipid molecules, and calculate order parameters for them.

$ gorder YOUR_INPUT_YAML_FILE

See the results of the analysis in order.yaml.

See the Gorder Manual for more information about using this program.

Features

Calculation of atomistic and coarse-grained order parameters for individual lipid types.
Simple atom selection using a VMD-like selection language, supporting regular expressions and groups from NDX files.
Automatic identification of bonds and topology-based classification of molecule types.
Output in YAML, XVG, CSV, and custom "table" format.
Scrambling-safe assignment of lipids to membrane leaflets using three different methods, and calculation of lipid order parameters for individual leaflets.
Calculation of order parameter maps.
Completely force-field agnostic.
Robust: use any XTC trajectory even with molecules broken at periodic boundaries.
Fast, multi-threaded analysis.

Planned

Robust error estimation using cross-validation.
Dynamic membrane normal calculation, supporting membrane vesicles.
Improved multithreading (currently, multithreading is only implemented at the trajectory reading level).
United-atom order parameters.
Python API: using gorder as a Python library.

Validation

🏗️ Work in progress... 🏗️

Rust API

gorder is also available as a Rust crate. See the gorder manual and the corresponding docs.rs page for more information.

License

The command line tool and the crate are both released under the MIT License.

Limitations

Only works for simulations with orthogonal simulation boxes.

gorder 0.2.0-beta