# Reference

Look-up material — flags, option keys, signatures.

## Command-line and input file

```{toctree}
:maxdepth: 1

cli
input-options
external-forces
nnp-options
```

## Python API

Auto-generated from source.

```{toctree}
:maxdepth: 1

acemd.acemd
acemd.protocols
acemd.utils
acemd.input
acemd.charmm
acemd.system
acemd.minimizer
acemd.nnp
acemd.restraints
acemd.reporters
acemd.licensing
acemd.versionwarnings
```

## Project metadata

```{toctree}
:maxdepth: 1

changelog
license
```