# Example 2: Biphasic Systems

## Example 2: Building Biphasic Systems

### Studay system

[![image.png](https://mccewiki.levich.net/uploads/images/gallery/2023-10/scaled-1680-/image.png)](https://mccewiki.levich.net/uploads/images/gallery/2023-10/image.png)

The original tutorial was to make a heterogeneous biphasic system composed of hydrophobic (cyclohexane) and hydrophilic (water) layers.

Here we are going to use benzene to replace cyclohexane as a demostration of how to use CHARMM-GUI to make a new ligand.

As we covered before, Gromacs simulations require two starting input files for a structure:

- Coordinate file: this can be a Protein Data Bank pdb file, or Gromacs
- Toplogy file: this can be a Gromacs top file

[![image.png](https://mccewiki.levich.net/uploads/images/gallery/2023-11/scaled-1680-/image.png)](https://mccewiki.levich.net/uploads/images/gallery/2023-11/image.png)

### Prepare benzene with CHARMM-GUI

#### Register a Charmm-GUI account

Go to [https://charmm-gui.org/](https://charmm-gui.org/) and register an account.

#### Model a molecule

Go to Ligand Reader and Modeler to search or create a molecule.