Packmol is a tool used to create initial configurations for molecular dynamics simulations. It packs molecules into defined regions of space while ensuring that short-range repulsive interactions do not disrupt the simulations.

To use Packmol, you must provide:

1. The coordinates of one molecule for each type.
2. The number of molecules for each type.
3. The spatial constraints that each molecule type must satisfy.

Packmol supports input files in PDB, TINKER, and XYZ formats.

You can use fpm to compile and install Packmol. This method automatically handles the executable installation into your PATH (typically ~/.local/bin on Linux).

1. Install fpm from the official installation guide.
2. Navigate to the packmol directory and run:

   fpm install --profile release

**Customizing the compiler:**
`fpm` uses `gfortran` by default. To use a different compiler (e.g., `ifort`), set the `FPM_FC` environment variable:
```bash
export FPM_FC=ifort

To compile Packmol from source using make:

1. Download the .tar.gz or .zip release from the GitHub releases page.
2. Unpack the archive:

   tar -xzvf packmol-VERSION.tar.gz

or

unzip -xzvf packmol-VERSION.zip

3. Navigate to the `packmol` directory, configure, and build (requires `gfortran` or another Fortran compiler):
   ```bash
   cd packmol
   ./configure [optional: path to fortran compiler]
   make

4. The packmol executable will be created in the main directory. Add this directory to your PATH to use it globally.

For most platforms, Packmol is available as a pre-built wheel on the Python Package Index. You can install it using pip.

pip install packmol

If you use uv, you can run Packmol directly as a CLI command without a manual installation step.

uvx packmol < inp.pack

The packmol Python package provides a command-line interface that acts as a wrapper around the compiled Packmol binary. When you call the packmol command in your terminal, it locates the appropriate platform-specific binary (e.g., packmol on Unix/Linux/macOS or packmol.exe on Windows) and executes it with the arguments you provide.

All arguments passed to the Python CLI are forwarded directly to the underlying Packmol executable.

# Example: Running packmol with an input configuration file
# (Note: The specific arguments depend on your Packmol input file content)
packmol input_file.inp