Molecular Dynamics Simulation Pipeline for Protein Analysis
This repository contains two versions of CHA-MD-BA:
- Original implementation in bash
- Scripts for MD simulation automation
- Designed for direct use with GROMACS
- New implementation in Python
- Improved command-line interface
- Additional features and comprehensive documentation
Complete documentation is available in:
- Bash Version:
bash_version/docs/ - Python Version:
python_version/docs/
This project is licensed under the MIT License - see the LICENSE file for details.
For questions and support, please open an issue in the GitHub repository.
CHA-MD-BA provides a complete pipeline for molecular dynamics simulations, including:
- Protein structure preparation
- Energy minimization
- NVT equilibration
- NPT equilibration
- Production runs
- Analysis tools
pip install cha-md-ba- Python 3.8+
- GROMACS 2022+
- NumPy
- MDAnalysis
- Rich
The package provides both a command-line interface and a Python API:
cha-md-ba prepare --input protein.pdb
cha-md-ba minimize
cha-md-ba nvt --force-constant 1000
cha-md-ba npt
cha-md-ba productionfrom cha_md_ba import prepare, minimize, nvt, npt
# Prepare the system
preparator = prepare.SystemPreparator("protein.pdb")
preparator.prepare()
# Minimize the system
minimizer = minimize.Minimizer()
minimizer.minimize()
# NVT equilibration
nvt_equilibrator = nvt.NVTEquilibrator()
nvt_equilibrator.equilibrate(force_constant=1000)
# NPT equilibration
npt_equilibrator = npt.NPTEquilibrator()
npt_equilibrator.equilibrate()Detailed documentation is available in the docs directory:
Contributions are welcome! Please read our Contributing Guidelines before submitting pull requests.
- GROMACS development team
- MDAnalysis developers
- All contributors to this project
Edgar Mixcoha