OpenCGChromatin: OpenMM implemented GPU-accelerated chemically specific chromatin model

Installation

1. Create a new conda environment and install OpenMM (with CUDA support):

   # Replace xx.x with your CUDA version (e.g., 11.2, 12.0)
   conda create -n opencg -c conda-forge openmm cuda-version=xx.x python=3.9
   conda activate opencg

2. Clone the repository and install:

   git clone https://github.com/CollepardoLab/OpenCGChromatin.git
   cd OpenCGChromatin
   pip install -e .
   

Citation

If you use any part of this code in your research, please cite: Russell, K., Chen, Y., Espinosa, J. R., Farre-Gil, D., Zhou, H., Maristany, M. J., Perez-Lopez, J. I., Huertas, J., Orozco, M., Rosen, M. K., Collepardo-Guevara, R (2025). Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation. https://doi.org/10.1101/2025.11.17.688899