# ACEMD

**High-performance GPU molecular dynamics with a minimal configuration surface.** Write a short YAML file, type `acemd`, and you're running production MD on your GPU. The same configuration covers classical force fields (CHARMM, AMBER, OpenMM XML), hybrid neural-network potentials (NNP/MM), and pure NNP simulations.

ACEMD integrates with [HTMD](https://software.acellera.com/htmd/) for system preparation and analysis from Python. Widely used in academic and industrial research — [700+ citations](https://pubs.acs.org/doi/abs/10.1021/ct9000685) — and free for non-commercial use, with [technical support](support.md) for both academic and commercial users.

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:::{grid-item-card} 🎓 Tutorials
:link: tutorials/index
:link-type: doc

Step-by-step lessons. Start here if you're new to ACEMD.
:::

:::{grid-item-card} 🛠 How-to guides
:link: how-to/index
:link-type: doc

Task-focused recipes. "How do I X?"
:::

:::{grid-item-card} 📖 Reference
:link: reference/index
:link-type: doc

CLI flags, input-file options, and the full Python API.
:::

:::{grid-item-card} 💡 Explanation
:link: explanation/index
:link-type: doc

Concepts and design rationale — what ACEMD does and why.
:::

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## Installation

```bash
pip install "acemd[cu13]"
```

See [Installation](installation.md) for CUDA-version matching, conda, and NNP-enabled variants.

## Quick start

Create an `input.yaml` describing the system and the run:

```yaml
structure: dhfr.prmtop
coordinates: dhfr.pdb
boxsize: [62.23, 62.23, 62.23]
thermostat: true
run: 10ns
```

Then start the simulation:

```bash
acemd
```

ACEMD writes the trajectory to `output.xtc`, log values to `output.csv`, and a checkpoint to `restart.chk`. See [tutorials/01-first-simulation](tutorials/01-first-simulation.md) for the full walkthrough.

## Support

Bug reports and questions go to [GitHub issues](https://github.com/Acellera/htmd/issues) for non-commercial users, or the [Acellera helpdesk](https://acellera.mojohelpdesk.com) for commercial users. See [Support](support.md) for details.

## Citing

If ACEMD is useful in your research, please cite:

M. J. Harvey, G. Giupponi, and G. De Fabritiis. *ACEMD: Accelerating biomolecular dynamics in the microsecond time scale.* J. Chem. Theory Comput. **2009**, 5 (6), 1632–1639. [doi:10.1021/ct9000685](https://pubs.acs.org/doi/abs/10.1021/ct9000685)

```{toctree}
:maxdepth: 1
:hidden:

installation
tutorials/index
how-to/index
reference/index
explanation/index
```