EasyMD is a Python package that simplifies molecular dynamics simulations, making them accessible to both beginners and experts. It provides an automated, easy-to-use interface for running protein-ligand simulations using OpenMM as the backend.

• Computational chemists who want to streamline their MD workflow
• Structural biologists studying protein-ligand interactions
• Drug discovery researchers analyzing binding dynamics
• Students and researchers learning molecular dynamics
• Anyone who wants to run MD simulations without dealing with complex setup

• Automated Setup: From structure preparation to production runs
• Integrated Force Fields: AMBER14 for proteins, OpenFF 2.0.0 for small molecules
• Flexible Configuration: Easy to customize simulation parameters
• Progress Monitoring: Real-time updates on simulation progress
• Analysis Tools: Built-in tools for RMSD, RMSF calculations

Follow our tutorial to learn how to use easy-md in quickrun mode. Run the interactive tutorial in Google Colab

First, install mamba, a fast package manager. You can use conda, but its extremely slow for some packages:

# If you have conda installed:
conda install mamba -n base -c conda-forge

# Or install mambaforge (standalone):
# For macOS/Linux:
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh

# For Windows:
# Download Mambaforge from:
# https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Windows-x86_64.exe

git clone https://github.com/ingcoder/easy-md.git
cd easy-md
mamba env create -f environment.yaml
mamba activate md_env
pip install -e 

from easy_md.main.quickrun import quickrun

# Run a simple protein-ligand simulation
quickrun(
    protein_file="path/to/protein.pdb",
    ligand_file="path/to/ligand.sdf",
    nsteps=1000
)

Core dependencies are automatically managed through pyproject.toml:

• Python >=3.9
• OpenMM >=7.7.0
• OpenFF-Toolkit >=0.11.0
• MDAnalysis >=2.4.0

Additional development dependencies are available in the conda environment.yaml file.

my_project/
├── config/
│   └── simulation_config.yaml  # Simulation parameters
├── structures/
│   ├── protein.pdb            # Input protein structure
│   └── ligand.sdf            # Input ligand structure
└── output/                    # Simulation outputs

This project is licensed under the MIT License - see the LICENSE file for details.

We welcome contributions! Please feel free to submit a Pull Request.