LAMMPS MCP server for AI agents

The MCP LAMMPS Server enables AI assistants to interact with LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) through natural language commands, allowing for setup, execution, and analysis of molecular dynamics simulations without requiring extensive programming knowledge.

Installation Requirements

Before installing the MCP LAMMPS Server, ensure you have:

Python 3.9 or higher
LAMMPS with Python interface

Installation Steps

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. Complete Installation

pip install -e .

Using the MCP LAMMPS Server

Starting the Server

To launch the MCP LAMMPS Server, run:

python -m mcp_lammps.server

Server Configuration

You can configure the server using environment variables:

export MCP_LAMMPS_LOG_LEVEL=INFO
export MCP_LAMMPS_WORK_DIR=/path/to/workspace
python -m mcp_lammps.server

Example Interactions

Once the server is running, you can interact with it using natural language commands. For example:

create a water simulation with 10 water molecules, save the relevant files, run the simulation at 300 K under NVT ensemble in the selected folder (examples)

This command will:

Set up a simulation with 10 water molecules
Configure the simulation to run at 300 K using the NVT ensemble
Save the simulation files in the specified folder
Execute the simulation

Core Features

Simulation Management

Create and configure LAMMPS simulations through natural language
Control simulation parameters (temperature, pressure, timestep, etc.)
Execute simulations and monitor progress

Structure Handling

Load molecular structures from various formats
Build simulation systems with specified compositions

Analysis Capabilities

Process simulation trajectories
Calculate thermodynamic properties
Extract insights from simulation data

Workflow Automation

Chain multiple simulation steps together
Create reusable simulation templates
Automate complex simulation protocols

How to install this MCP server

For Claude Code

To add this MCP server to Claude Code, run this command in your terminal:

claude mcp add-json "mcp-lammps" '{"command":"python","args":["-m","mcp_lammps.server"]}'

See the official Claude Code MCP documentation for more details.

For Cursor

There are two ways to add an MCP server to Cursor. The most common way is to add the server globally in the ~/.cursor/mcp.json file so that it is available in all of your projects.

If you only need the server in a single project, you can add it to the project instead by creating or adding it to the .cursor/mcp.json file.

Adding an MCP server to Cursor globally

To add a global MCP server go to Cursor Settings > Tools & Integrations and click "New MCP Server".

When you click that button the ~/.cursor/mcp.json file will be opened and you can add your server like this:

{
    "mcpServers": {
        "mcp-lammps": {
            "command": "python",
            "args": [
                "-m",
                "mcp_lammps.server"
            ]
        }
    }
}

Adding an MCP server to a project

To add an MCP server to a project you can create a new .cursor/mcp.json file or add it to the existing one. This will look exactly the same as the global MCP server example above.

How to use the MCP server

Once the server is installed, you might need to head back to Settings > MCP and click the refresh button.

The Cursor agent will then be able to see the available tools the added MCP server has available and will call them when it needs to.

You can also explicitly ask the agent to use the tool by mentioning the tool name and describing what the function does.

For Claude Desktop

To add this MCP server to Claude Desktop:

1. Find your configuration file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
Windows: %APPDATA%\Claude\claude_desktop_config.json
Linux: ~/.config/Claude/claude_desktop_config.json

2. Add this to your configuration file:

{
    "mcpServers": {
        "mcp-lammps": {
            "command": "python",
            "args": [
                "-m",
                "mcp_lammps.server"
            ]
        }
    }
}

3. Restart Claude Desktop for the changes to take effect