MD-Agent is a LLM-agent based toolset for Molecular Dynamics. It's built using Langchain and uses a collection of tools to set up and execute molecular dynamics simulations, particularly in OpenMM.
To use the OpenMM features in the agent, please set up a conda environment, following these steps.
- Create conda environment:
conda env create -n mdagent -f environment.yaml - Activate your environment:
conda activate mdagent
If you already have a conda environment, you can install dependencies with the following step.
- Install the necessary conda dependencies:
conda install -c conda-forge openmm pdbfixer mdtraj
pip install git+https://github.com/ur-whitelab/md-agent.git
The first step is to set up your API keys in your environment. An OpenAI key is necessary for this project. Other tools require API keys, such as paper-qa for literature searches. We recommend setting up the keys in a .env file. You can use the provided .env.example file as a template.
- Copy the
.env.examplefile and rename it to.env:cp .env.example .env - Replace the placeholder values in
.envwith your actual keys
If you'd like to use MDAgent via the streamlit app, make sure you have completed the steps above. Then, in your terminal, run streamlit run st_app.py in the project root directory.
From there you may upload files to use during the run. Note: the app is currently limited to uploading .pdb and .cif files, and the max size is defaulted at 200MB.
- To upload larger files, instead run
streamlit run st_app.py --server.maxUploadSize=some_large_number - To add different file types, you can add your desired file type to the list in the streamlit app file.
We welcome contributions to MD-Agent! If you're interested in contributing to the project, please check out our Contributor's Guide for detailed instructions on getting started, feature development, and the pull request process.
We value and appreciate all contributions to MD-Agent.