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Welcome to m2dtools Documentation

m2dtools is a lightweight Python toolkit for molecular simulation workflows, providing utilities for structure handling, trajectory analysis, coarse-graining, and LAMMPS interfacing. It is designed to support multiscale molecular modeling with simple, modular components that can be used independently or combined into automated pipelines.

Features

  • Structure and trajectory utilities
    Read, write, filter, and manipulate molecular data with minimal overhead.

  • Coarse-graining support
    Tools for computing RDFs, bonded distributions, and preparing inputs for CG force-field optimization workflows.

  • LAMMPS helpers
    Read full-style data files, extract atom and topology information, and prepare simulation inputs.

  • Network and graph tools
    Construct connectivity networks, compute graph-based descriptors, and analyze polymer or molecular connectivity.

  • Modular design
    Each submodule is self-contained, making it easy to integrate with existing workflows in MD, CGMD, or ML-accelerated simulations.

Installation

pip install m2dtools

Or install from source:

git clone https://github.com/zyumse/m2dtools
cd m2dtools
pip install -e .