rutherfordb-1 / analysis

Analysis scripts for molecular dynamics simulations of stratum corneum lipid multilayers.

Analysis

Analysis scripts for molecular dynamics simulations of stratum corneum lipid multilayers.

Installation Instructions

The package can be installed via pip

1. Clone the repository

git clone https://github.com/uppittu11/analysis.git

2. Install the package

cd analysis
pip install -e .

3. Run tests for the package

pytest -v analysis

I suggest you install this package in a separate conda environment so the analyze command does not clobber anything in your default namespace

Usage

To calculate basic structural properties (tilt angle, repeat distance, nematic order, and area per lipid) using a parallel multiprocessing pool, use the bash command analyze.

Command line arguments for analyze

-f trajectory file (needs to be a format loadable by MDTraj)

-c topology file (needs to be a format loadable by MDTraj)

-o output directory

-n number of leaflets

--cg use this flag to denote a coarse-grain system

--reload use this flag to ignore cached trajectory (typically located in the output directory)

--min minimum z position of lipid headgroups to include in analysis

--max maximum z position of lipid headgroups to include in analysis. Use --min and --max to specify one or more layers in a multilayer system

Loading in results

analysis will output a pickled dictionary file containing structural properties calculated for each frame of the trajectory (default: outputDirectory/results.p. This output file can be loaded and analyzed using functions in the analysis.data module.

Currently Supported Measurements

• Tilt Angles
• Bilayer/Multilayer Height
• Nematic Order Parameter
• Area per Lipid