s-gordon/md-tat

Wrapper scripts around MDTraj and VMD for analysing and plotting molecular dynamics simulations.

Molecular Dynamics Trajectory Analysis Tools (MD-TAT)

Version

Alpha 0.10

Introduction and Foreword

You are free to use it, but it may not be entirely suitable for what you are trying to achieve. Please email feedback, bugs or suggestions to: [email protected].

Dependencies

• Python (v2.7+)
• MDtraj
• Matplotlib

Installation

The best way is using pip:

pip install mdtat

Alternatively, clone the repo from github and install using distutils:

git clone https://github.com/s-gordon/md-tat
cd md-tat
python setup.py install

How it all works

This project directory is designed to be used at the completion of a run as a place to consolidate and process trajectory data generated using the workflow MD_workflow. You'll need to point compress.py in the right direction of the trajectory files relative to where you run these scripts.

Trajectory processing and analysis are divided into three main phases divided into two independent scripts: compress.py, and analyze_plot.py. The order in which these scripts are run is critical.

1. compress.py: Additional options, such as trajectory sub-sampling (a.k.a. stride) can be passed as optional arguments. For more information try ./compress.py --help.

2. analyze_plot.py: Options can be passed as arguments. For more information try ./analyse_plot.py --help.

Authorship

• Shane Gordon [email protected].