This repository contains a collection of Python scripts for analyzing molecular dynamics (MD) simulations of protein-membrane systems. The tools are written to work with the MDAnalysis library and are primarily designed for Coarse-Grained (CG) simulation data.
Here are some examples of the plots this toolkit can generate, placed side-by-side for a cleaner look.
| Membrane Properties | Lipid Order Parameters |
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Click to expand the full list of analysis functions
This collection provides functions to perform a wide range of common and advanced membrane analyses:
- 2D Density Maps: Calculate spatial density maps for lipids or other molecules in the X-Y or X-Z planes.
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Leaflet Identification: Includes two robust methods for assigning lipids to leaflets:
- A fast, Z-coordinate-based midplane method.
- An advanced DBSCAN clustering method for curved or disrupted membranes.
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Membrane Thickness & Curvature:
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calculate_membrane_thickness: Uses Radial Basis Functions (RBF) to create a smooth surface map of local membrane thickness. -
calculate_mean_curvature: Computes the mean curvature (H) across the membrane surface.
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Lipid Order & Dynamics:
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calculate_scd_profile: Calculates deuterium order parameters ($S_{CD}$ ) for various Martini lipids from a built-in library. -
calculate_lipid_tilt_angle: Tracks the orientation of a single lipid throughout a trajectory, useful for analyzing flipping events.
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Interaction Analysis:
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parallel_contacts_within_cutoff: A highly efficient, parallelized function to calculate the number of contacts between two molecular groups over time.
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To use these scripts, you will need a Python environment with the following major packages installed.
pip install mdanalysis numpy pandas scikit-learn scipy matplotlib tqdm