Welcome to MembraneCurvature’s Documentation

Minimum MDAnalysis version: 1.1.1

Last updated: Jan 28, 2024

The MDAnalysis MembraneCurvature tool module calculates the Gaussian and mean curvature from Molecular Dynamics (MD) simulations.

MembraneCurvature derives 2D curvature profiles of a surface of reference. To suit the needs of your system, we offer flexible atom selection that will enable you to use the most convenient AtomGroup to extract curvature from your MD simulations!

This is an example on how to use MembraneCurvature:

import MDAnalysis as mda
from membrane_curvature.base import MembraneCurvature

u = mda.Universe(coordinates, trajectory)
mc = MembraneCurvature(u).run()

surface =  mc.results.average_z_surface
mean_curvature =  mc.results.average_mean_curvature
gaussian_curvature = mc.results.average_gaussian_curvature

You can find more details on how to use MembraneCurvature in the Usage page.

Features

MembraneCurvature calculates mean and Gaussian curvature from MD simulations in:

1. Monolayers.

2. Membrane-only systems.

3. Membrane-protein systems.

Why MembraneCurvature?

MembraneCurvature is a user-friendly, actively-maintained, well-documented tool in Python 3 to derive 2D maps of membrane curvature from MD Simulations, using the most recent version of MDAnalysis Are you interested in calculating mean and Gaussian curvature from MD simulations? This tool is for you!

Installation

The main dependency in MembraneCurvature is MDAnalysis. You can find instructions to install the latest stable version of MDAnalysis via conda in the Installation Quick Start page.

MembraneCurvature is available via pip:

pip install membrane-curvature

To install from source:

git clone https://github.com/MDAnalysis/membrane-curvature.git
cd membrane-curvature
conda env create -f devtools/conda-envs/environment.yaml
conda activate membrane-curvature
python setup.py install

Some of the examples included in the MembraneCurvature documentation use test cases from MDAnalysis Tests. To install the unit tests via conda:

conda install -c conda-forge MDAnalysisTests

or via pip:

pip install --upgrade MDAnalysisTests

Contents:

• Getting Started
  • Installation
• MembraneCurvature’s API Documentation
  • MembraneCurvature
  • MembraneCurvature
  • Curvature
  • gaussian_curvature()
  • mean_curvature()
  • Surface
  • derive_surface()
  • get_z_surface()
  • normalized_grid()
• Algorithm
  • Overview
  • 1. Select atoms of reference
  • 2. Set grid
  • 3. Derive surface and calculate curvature
  • 4. Average over frames
• Usage
  • 1. Membrane-only systems
  • 2.1 Membrane-protein systems
  • 2.1.1 Membrane-protein systems, protein with position restraints
  • 2.1.2. Membrane-protein systems, protein with no position restraints
• Visualization
  • 1. imshow
  • 2. contourf
• Tutorials
  • Membrane-only systems
  • Membrane-protein systems

License

Source code included in this project is available under the GNU Public License v3 from github.com/MDAnalysis/membrane_curvature.

Indices and tables

• Index

• Module Index

• Search Page