MDFactoryMDFactory

MDFactory

High-throughput molecular dynamics simulation library

MDFactory is an open source, end-to-end simulation manager for high-throughput molecular dynamics with robust data management. It handles the full pipeline from molecular structure generation through parametrization, system building, simulation, and analysis — with built-in database integration for tracking results at scale.

MDFactory pipeline: CSV/YAML input → Structure Generation (RDKit) → Parametrization (OpenFF, CGenFF) → System Build (Mixedbox, Bilayer, LNP) → Simulation (GROMACS, OpenMM) → Analysis, with Database sync to Simulation DB and Analysis DB

Batch Processing

CSV-driven: one row = one system. Run hundreds of systems in parallel via Nextflow on HPC.

Modular Pipeline

Pluggable build types (mixedbox, bilayer, LNP) with swappable force fields (OpenFF, CGenFF).

Analysis Framework

11+ registered analysis types with parquet + JSON metadata output and extensible registry.

Data Integration

SQLite, CSV, and Palantir Foundry backends with intelligent push/pull/sync via CLI.

Getting Started

Installation

Install the package and verify the CLI

Quick Start

Build a simple mixed-box system

Configuration

Configure storage, backends, and runtime paths

Core Guides

Executing Analyses

Run registered analyses and artifacts

20-System Tutorial

Hands-on campaign with SQLite sync and notebook aggregation

Foundry Dev Tools

Configure and use the Foundry backend

Architecture

Understand the current code structure

Installation

Install MDFactory for production use or development

On this page

Getting StartedCore Guides