2. Prepare a directory for a NEMAT run: nemat start

Create a new empty directory and, inside the directory, use:

nemat start

This will copy into your directory the following elements:

1. A folder named membrane

2. A folder named proteins

3. A folder named mdppath

4. A folder named ligands

5. A folder named logs

6. A file named input.yaml

Now you have the structure to start a NEMAT run. You need to fill the input.yaml file with the parameters for your run (see here).