lecules to include inside the box. This can be modified with the flag <code>--gcmcwater</code>. The amount of waters included as JAWS probes can have an effect in the results of your simulation. Feel free to play around with this parameter. It can be specified as shown below </p>
<p><pre>
python $PROTOMSHOME/protoms.py -l fragment.pdb -p protein.pdb -s jaws1 -c big --gcmcbox 59 31 23 8 8 8 --gcmcwater 10
</pre></p>
<p>
<h5>Running longer simulations</h5>
There are two arguments that you can invoke to run a 