The program as well as document and a tutorial is avialable on the GitHub.
COBY is a Python-based software for building flat membranes in coarse-grained resolution. It handles asymmetric membranes, phase-separated systems, multiple bilayers, protein insertion, solvation and flooding with one or multiple solute molecules of choice.
COBY is versatile, fast, easy-to-use, but it also allows for high-level of customisation. It can be used either as a Python package or directly from the terminal command line. It neatly handles multiple parameter libraries (even within the same system), making it developer-friendly.
COBY is continuously under development and we welcome suggestions for new features.
Andreasen et al. (2024) TBD.
Version 1 - Using pip (requires python>=3.9)
conda create --name COBY python==3.9 ipykernel
conda activate COBY
pip install COBY
python -m ipykernel install --user --name=COBY
Ipykernel allows the user to use COBY environment within the Jupyter notebook.
For a detailed introduction to the software, please consult COBY Documentation.
For a quick reminder of available commands, you can use the Cheat Sheet.
Two tutorials are available as Jupyter Notebooks, one covering the basics and another covering more advanced functionalities.
It includes (amongst other systems):
- Simple membrane with protein: A simple POPC membrane with a protein in solvent (water + 0.15 M NaCl) which explains the various arguments in COBY
- Asymmetric membrane: An asymmetric complex membrane (POPC, POPE and CHOL) in solvent with different area per lipid values for each membrane
- Phase separated Membrane: A phase separated membrane
- Monolayers: Two monolayers with solvent between them and vacuum over the pbc
- Nanodisc: A nanodisc with DMPC lipid contained within and with solvent surrounding it
- Holes: A membrane with multiple manually defined holes
- Patches: Multiple manually shaped membrane patches
- Matryoshka membrane: A matryoshka membrane with a protein in the center
- Stacked membranes: Three vertically stacked membranes
- Mixed solvent: A symmetric membrane solvated with regular and small water beads in specified ratios
- Phase separated solvent: A symmetric membrane solvated with two solvent volumes containing different salt concentrations
- Flooding of imported solutes: A membrane system that has been flooded with imported solute molecules, followed by solvation
- COBY logo: Our logo
COBY is preserved under the Apache License 2.0.
