polychrom-hoomd

HOOMD-blue-based package for coarse-grained polymer and chromosome simulations.

Installation

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-hoomd

Note 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 .

Usage

See the attached Jupyter notebook tutorials within the examples directory.