A Python package for analyzing rotational diffusion from molecular dynamics simulations.
- Determine the orientation of a molecule along an MD trajectory
- Compute rotational correlation functions
- Analyze time-dependent rotational diffusion behaviour
- Fit a Brownian rotational diffusion model to the rotational correlation functions
- Estimate uncertainties of the obtained principal axes and diffusion coefficients
First, clone this repository using
git clone https://github.com/MolSimGroup/rotationaldiffusion.git
Then, cd into the cloned directory and install the package using pip
pip install .
We suggest to use the package by importing it as
import RotationalDiffusion as rd
The full documentation is available at: https://rotationaldiffusion.readthedocs.io
A slightly older but comprehensive tutorial demonstrating the main functionalities of the package is included in the documentation. Further, a user guide and more advanced API documentation are currently being developed.
If you use this package in your research, please read and cite
S. L. Holtbrügge and L. V. Schäfer: Robust Estimation of Rotational Diffusion Tensors of Proteins from Molecular Dynamics Simulations, 2025. bioRxiv, doi: 10.1101/2025.05.27.656261.
This package was developed by Simon Holtbrügge. Contact: simon.holtbruegge@rub.de.
This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.