HOOMD-blue-based package for coarse-grained polymer and chromosome simulations.
You may use the provided environment.yml file to create a conda environment polychrom-hoomd including all required software packages:
conda env create -f environment.yml
conda activate polychrom-hoomdNote that this environment should be built on a node with GPU access (and CUDA). HOOMD may silently default to CPU version if this is not the case.
Following which the code may be installed as usual,
python3 -m pip install -e .See the attached Jupyter notebook tutorials within the examples directory.