mdfs

MD from scratch

Author: Zhaoyang Li
Published: October 30, 2025

Installation

1. Install miniconda following the instructions here.
2. Then run the following commands to setup the environment in the repo root directory:

# Create a conda environment
conda create -n mdfs python=3.12 --yes
conda activate mdfs

# Install uv
pip install uv

# Install required packages with correct versions
uv pip install -e .[dev]

For systems equipped with NVIDIA GPUs, CUDA-enabled versions of JAX and OpenMM (compatible with CUDA 12) can be installed using:

uv pip install -e .[dev,cuda12]

---

To validate your installation is successful, you may simply run pytest.

Let's start now!

See Also

• JAX, M.D.: Differentiable, Hardware Accelerated, Molecular Dynamics
• OpenMM: OpenMM is a toolkit for molecular simulation using high performance GPU code.
• MDTraj: An open library for the analysis of molecular dynamics trajectories