script to setup a JAWS stage 1 simulation. The <code>-p</code> and <code>-l</code> arguments specifies the protein and the ligand, respectively.
</p> 
You can read more about the files that the setup script creates further down on this <a href="#files">page</a>.
<p>You can visualise the systems that will be simulated with for instance VMD:
<pre>vmd -m protein.pdb fragment.pdb water_clr.pdb jaws1_wat.pdb jaws1_box.pdb</pre>
<p>
<img src="setup.png"  alt="" />
</p>
</p>
<p> 
<h5>Execution</h5>
To run the simu