ns in VMD. It is probably interesting to display only the most populated clusters by showing only <code> resid 1 to 5 </code>, for example, since clusters are assigned residue ID in order of most populated clusters.
</p>
<img src="cluster.png"  alt="" />
<p> 
<h3>Exploring more options</h3>
<p>
<h5>Running JAWS on different areas of your simulation</h5>
By running <code>protoms.py</code> as above, protoms will try to locate the waters found in a box with edges at least 2A away from any of your ligand atoms.