# Run a pure NNP simulation

**You will learn:** how to simulate a system in which **every** atom is described by a neural-network potential, with no classical force field involved.

**Prerequisites:**

- ACEMD installed with NNP support.
- A structure file in any of: PDB, CIF, BCIF, SDF, MOL2. **No** classical topology is needed.

## Setup

Worked example: benzamidine in vacuum, all-AceFF. Download {download}`benzamidine_nnp.zip <../benzamidine_nnp.zip>` for the input file.

```{code-block} yaml
:caption: input.yaml

thermostat: true
thermostattemperature: 300
velocities: 300
structure: BEN_pH7_4.cif
coordinates: BEN_pH7_4.cif
minimize: 500
timestep: 2
run: 2ns
nnp:
  name: AceFF-2.0
  type: torch
```

The `nnp` block has **no `sel`** — that's what makes it a pure NNP simulation. ACEMD applies the NNP to every atom. ACEMD auto-downloads AceFF-2.0 from HuggingFace on first use and caches it under `~/.cache/acemd/nnp/`. See [Obtain AceFF NNP models](obtain-aceff-models.md) if you need to manage the checkpoint manually.

## Run

```bash
acemd
```

## Why no classical topology?

In NNP/MM mode you need a PSF / PRMTOP because the rest of the system has to be parameterised classically. In pure-NNP mode there is no "rest of the system" — the NNP supplies all forces — so any file that gives atom positions and elements is enough. Use PDB / CIF / SDF / MOL2 directly.

## Parameters that matter

- **`timestep`** — 2 fs is the recommended maximum. NNPs are less numerically stable than classical force fields.
- **`nnp.name`** — model identifier. Use `"AceFF-2.0"` to auto-download the latest AceFF, or `"TorchMD-Net"` if you're providing a checkpoint path via `nnp.file`.
- **`nnp.file`** — optional. Only set when supplying a TorchMD-Net checkpoint manually.

See [NNP options](../reference/nnp-options.md) for the full reference.

## Gotchas

- **AceFF 2.0 is small-molecule only.** Don't pure-NNP a protein, nucleic acid, or solvent box — those species are outside the training distribution. For mixed systems, use [NNP/MM](run-an-nnp-mm-simulation.md) and keep `nnp.sel` on the small molecule.
- **AceFF 2.0 supports total charges of -2 to +2.** Other charges produce wrong forces.
- **If the simulation crashes, drop `timestep` to 1 fs.** Either that, or wrap the species in classical solvent and switch to [NNP/MM](run-an-nnp-mm-simulation.md).

## See also

- [Run an NNP/MM simulation](run-an-nnp-mm-simulation.md)
- [Obtain AceFF NNP models](obtain-aceff-models.md)
- [NNP options reference](../reference/nnp-options.md)
- [NNP and NNP/MM concepts](../explanation/nnp-and-nnp-mm.md)