flowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics

flowerMD is a modular “wrapper” package for molecular dynamics (MD) simulation pipeline development, designed to enable fast, reproducible, end-to- end simulation workflows with minimal user effort. This package is a wrapper for MoSDeF packages and Hoomd-Blue with a focus on simulating soft matter systems.

An object-oriented design makes flowerMD extensible and highly flexible. This is bolstered by a library-based approach to system initialization, making flowerMD agnostic to system identity, forcefield, and thermodynamic ensemble, and allowing for growth on an as-needed basis.

flowerMD's design allows for creation of modules where an end-to-end interface is designed with a complex task in mind, such as fusion welding of polymers and surface wetting:

Installing flowermd

Installing flowermd from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, flowermd can be installed with conda:

conda install flowermd

or with mamba:

mamba install flowermd

Installing from source for development:

Clone this repository:

git clone git@github.com:cmelab/flowerMD.git
cd flowerMD

Set up and activate environment:

conda env create -f environment-dev.yml
conda activate flowermd-dev
python -m pip install -e .

A note on GPU compatibility:

To install a GPU compatible version of HOOMD-blue in your flowerMD environment, you need to manually set the CUDA version before installing flowermd. This is to ensure that the HOOMD build pulled from conda-forge is compatible with your CUDA version. To set the CUDA version, run the following command before installing flowermd:

export CONDA_OVERRIDE_CUDA="[YOUR_CUDA_VERSION]"

Basic Usage

Please check out the tutorials for a detailed description of how to use flowerMD and what functionalities it provides.

Documentation

Documentation is available at https://flowermd.readthedocs.io

Citing flowerMD

If you use flowerMD in your research, please cite the following paper:

Albooyeh, M., Jones, C., Barrett, R., & Jankowski, E. (2023). FlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics. Journal of Open Source Software, 8(92), 5989, https://doi.org/10.21105/joss.05989

Contributing to flowerMD

We welcome all contributions to flowerMD. Please see contributing guidelines for more information.