 generated. It will contain 10 water molecules (flag <code>-m</code>). The box dimensions to which the waters will be constrained are specified with the flag <code>-b</code>, and this information on the box limits is stored in the first line of the <code>jaws1_water.pdb</code> file.
<li>The last step in this section consists of clearing the water molecules from the solvation droplet which overlap with the JAWS-box. Do this by typing:
<pre>python $PROTOMSHOME/tools/clear_gcmcbox.py -b jaws1_wat.pdb -s water.