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MDCraft

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What MDCraft is

MDCraft is a free, GPL-3.0 Python assistant for molecular-dynamics research on soft-matter systems. It supports simulation setup and execution, trajectory analysis, modeling, fitting, and plotting for scientific publications. High-level analysis classes serve end users, while serial and parallel tools built on MDAnalysis support data analysis. Its algorithm module provides Numba, NumPy, and SciPy routines for data handling and structural or dynamical properties. OpenMM helpers cover coarse-grained simulations with reduced units, custom bond and pair potentials, NetCDF trajectories, and a Gaussian Core Model with smeared electrostatics. MDCraft also includes LAMMPS setup helpers, trajectory reading, and topology utilities. The fit module offers two-dimensional SciPy curve-fitting models, and the plot module adds Matplotlib functionality for publication-ready figures. It runs on Linux, macOS, and Windows and requires Python 3.9 or later. Installation is available through PyPI, Anaconda, or source using pip or Conda/Mamba.

Who it suits

MDCraft is aimed at molecular-dynamics researchers, with approachable analysis classes for end users and direct algorithm access for experienced programmers.

What it does well

Free GPL-3.0 project
Linux, macOS, and Windows support
OpenMM and LAMMPS helpers
MDAnalysis-based serial and parallel analysis
Matplotlib publication-ready plotting

What to know first

Requires Python 3.9 or later
Pip OpenMM users must build OpenMM
Image-charge method needs an additional plugin
Curated examples are still a work in progress

Verdict

MDCraft covers a broad simulation-to-publication workflow and supports several molecular-dynamics tools. OpenMM setup can require extra compilation or plugins, so installation choices should be planned around the intended features.

Facts from MDCraft's own pages

Algorithms: Its algorithm module provides Numba, NumPy, and SciPy algorithms for data wrangling and evaluating structural and dynamical properties. · github.com, 12 Oct 2026
Analysis: Its analysis tools include high-level classes and low-level optimized algorithms for calculating properties from simulation data. · mdcraft.readthedocs.io, 5 Oct 2026
Analysis tools: Its analysis module provides serial and parallel data analysis tools built on the MDAnalysis framework. · github.com, 12 Oct 2026
Audience: The documentation presents MDCraft for molecular-dynamics researchers, with high-level analysis classes for end users and direct access to optimized algorithms for more experienced programmers. · mdcraft.readthedocs.io, 12 Oct 2026
Fitting and plotting: The fit module provides two-dimensional curve-fitting models for SciPy, and the plot module adds settings and functionality for Matplotlib figures. · github.com, 12 Oct 2026
Free plan: Yes · mdcraft.readthedocs.io, 24 Sept 2026
Gaussian Core Model: MDCraft provides a Gaussian Core Model with smeared electrostatics force field, and its documentation highlights computational speed-up when used with OpenMM. · github.com, 12 Oct 2026
Image charge dependency: Using the OpenMM image-charge method requires installing constvplugin or openmm-ic-plugin. · mdcraft.readthedocs.io, 5 Oct 2026
Image charges requirement: Using the OpenMM image-charges method requires compiling and installing either constvplugin or openmm-ic-plugin. · mdcraft.readthedocs.io, 12 Oct 2026
Install options: MDCraft can be installed with pip, Conda, or Mamba, or from source, and requires Python 3.9 or later. · mdcraft.readthedocs.io, 12 Oct 2026
Integrations: The documentation describes OpenMM simulation helpers and a LAMMPS trajectory reader and topology utilities. · mdcraft.readthedocs.io, 5 Oct 2026
License: The project repository identifies MDCraft as licensed under GPL-3.0. · github.com, 12 Oct 2026
Maker: The documentation copyright names Benjamin Ye and Pierre Walker; the opened pages do not state a company name or headquarters. · mdcraft.readthedocs.io, 5 Oct 2026
OpenMM prerequisite: Users installing with pip who plan to use OpenMM must compile and build OpenMM themselves; Conda/Mamba users can install it through those package managers. · mdcraft.readthedocs.io, 5 Oct 2026
OpenMM requirement: When installing with pip, users planning to use OpenMM must compile and build OpenMM themselves; Conda or Mamba instructions are provided for installing it. · mdcraft.readthedocs.io, 12 Oct 2026
OpenMM support: The OpenMM submodule provides helpers for setting up simulations, including coarse-grained simulations with reduced units. · mdcraft.readthedocs.io, 5 Oct 2026
Plotting: The plot submodule supports visualizing analysis results in publication-ready figures using Matplotlib. · mdcraft.readthedocs.io, 5 Oct 2026
Purpose: MDCraft is a Python assistant for performing and analyzing molecular dynamics simulations of soft matter systems. · mdcraft.readthedocs.io, 12 Oct 2026
Python requirement: MDCraft requires Python 3.9 or later. · mdcraft.readthedocs.io, 5 Oct 2026
Research workflow: The documentation describes MDCraft as supporting simulation setup and execution, trajectory analysis, modeling, and plotting data for scientific publications. · mdcraft.readthedocs.io, 12 Oct 2026
Security: The opened documentation and repository pages provide no stated security or compliance commitments. · mdcraft.readthedocs.io, 5 Oct 2026
Simulation integrations: MDCraft includes helper functions for setting up LAMMPS simulations and extensions to OpenMM, including custom bond and pair potentials and NetCDF trajectory support. · github.com, 12 Oct 2026
Support and contributions: The project invites questions in GitHub Discussions, bug reports and feature requests through issues, and contributions through pull requests. · github.com, 5 Oct 2026
Tutorial status: The documentation labels its curated user-guide examples as a work in progress. · mdcraft.readthedocs.io, 12 Oct 2026

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