Introduction

HeddleMD is a molecular dynamics engine for simulating condensed-phase systems — liquids, solutions, and solvated biomolecules — on a single NVIDIA GPU. You describe a system with a force field, a starting configuration, and a thermodynamic ensemble, and the engine propagates it in time and writes a trajectory you can analyse.

Out of the box you can:

• Run NVE, NVT, and NPT dynamics, with a choice of thermostats (Nosé-Hoover chains, CSVR, Andersen, Berendsen) and barostats (stochastic cell-rescale, Monte-Carlo, Berendsen).
• Build a force field from Lennard-Jones van der Waals terms, smooth particle-mesh Ewald (SPME) electrostatics, and bonded interactions (harmonic and Morse bonds, harmonic angles, periodic torsions) with automatic 1-2/1-3 exclusions and 1-4 scaling.
• Keep water and other rigid groups rigid with SETTLE or SHAKE/RATTLE constraints, so you can take the longer timesteps those force fields assume.
• Minimize a starting structure before sampling, then chain multiple phases (equilibration followed by production) in a single run.
• Post-process trajectories in place with heddlemd analyze — the radial distribution function ships built-in.

Every quantity that affects the physics is set in a human-readable TOML file, in SI units by default, and inputs can be checked on a login node with heddlemd lint before a job reaches the queue.

Reproducibility

A distinguishing feature of HeddleMD is bit-wise reproducibility: rerun the same input on the same GPU and you get a byte-identical trajectory and log, every time. This makes debugging, regression testing, and sharing an exact result with a collaborator straightforward. The scope and limits of the guarantee are spelled out in Reproducibility.

What’s in this book

• Getting Started walks through installation and running the bundled 10,000-atom Lennard-Jones argon example.
• User Guide covers building your own simulation: the TOML config, the extended-XYZ starting-structure file, output formats, trajectory analysis, and what reproducibility does and does not guarantee.
• Reference documents the command-line interface.

This book is the user-facing guide; its Developer Guide is for contributors working on the engine itself. It frames the engine’s internal design — the GPU compute pipeline and the deterministic-reduction strategy — and, in its Extending HeddleMD sub-section, walks through adding new physics such as thermostats, integrators, barostats, and pair or bonded potentials. The exhaustive design reference lives in docs/architecture.md in the repository.