MCP LAMMPS Server

A Model Context Protocol (MCP) server that enables AI assistants to interact with LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) for molecular dynamics simulations.

Status

This is still in experimental status. This package is developed in collaboration with AI coder.

Update 06.12.2025

Note: all tests are performed with Sonnet 4.5

Add support for organic liquids simulations with gaff

simple test prompt:

Organic Liquid Simulation

Multi-Component Simulation

Related MCP server: MCP Toolkit

Overview

This MCP is part of our workflow for the autonomous computational materials design with LLM. This MCP server provides a standardized interface for controlling LAMMPS molecular dynamics simulations through natural language commands. It enables AI assistants to:

• Set up and configure molecular dynamics simulations

• Run equilibration and production simulations

• Monitor simulation progress in real-time

• Analyze simulation results

• Manage simulation workflows

Features

Core Capabilities

• Simulation Management: Create, configure, and run LAMMPS simulations

• Molecular Structure Processing: Convert SMILES to 3D structures, assign GAFF atom types

• Force Field Support: GAFF (General AMBER Force Field) parameter assignment

• LAMMPS Data File Generation: Create simulation input files from molecular structures

• Real-time Monitoring: Track simulation progress and system properties

• Analysis Tools: Process trajectories and calculate thermodynamic properties (with MDAnalysis)

• Charge Calculation: Gasteiger, MMFF94, and GAFF charge estimation methods

• Workflow Automation: Define and execute multi-step simulation workflows

• SLURM Integration: Submit and manage simulations on HPC clusters (optional)

Supported Molecular Systems

• Small organic molecules

• Liquid systems and mixtures

• Polymer systems

• Custom molecular structures via SMILES or coordinate files

Installation

Prerequisites

• Python 3.9 or higher

• LAMMPS with Python interface

• RDKit (for molecular structure processing)

• Packmol (for organic liquid box creation with proper molecular packing)

System Dependencies

Packmol Installation (Required for organic liquid simulations):

Optional Dependencies

• MDAnalysis (for advanced trajectory analysis)

• OpenBabel (for additional molecular format conversion - requires system Open Babel libraries)

• pytraj (for additional trajectory analysis - requires cpptraj)

• SLURM (for HPC cluster job submission and management)

Quick Start

1. Clone the repository:

   git clone https://github.com/mcp-lammps/mcp-lammps.git cd mcp-lammps

2. Create a virtual environment:

   python -m venv venv source venv/bin/activate # On Windows: venv\Scripts\activate

3. Install dependencies:

   pip install -r requirements.txt

4. Install in development mode:

   pip install -e .

Usage

Basic Usage

Start the MCP server:

Configuration

The server can be configured through environment variables or configuration files:

SLURM Cluster Integration

For HPC cluster environments, MCP LAMMPS supports SLURM job submission:

1. Configure slurm_config.yaml in your workspace:

2. Submit simulations to SLURM cluster via AI commands or programmatically

See SLURM Integration Guide for detailed instructions.

Example Prompts

Basic Organic Molecule Simulation:

Multi-Component Mixture:

Custom Molecule from SMILES:

Development

Project Structure

Contributing

1. Fork the repository

2. Create a feature branch

3. Make your changes

4. Add tests for new functionality

5. Ensure all tests pass

6. Submit a pull request

License

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

Acknowledgments

• LAMMPS development team for the molecular dynamics engine

• Model Context Protocol community for the MCP framework

• Scientific computing community for inspiration and feedback

• LLM for writing the code