longer simulation
<ul>
	<li><code>--nequil</code> - this controls the number of equilibration steps</li>
	<li><code>--nprod</code> - this controls the number of production steps</li>
</ul>  
by typing for instance
<p>
<pre>python $PROTOMSHOME/protoms.py -s jaws1 -p protein.pdb -l fragment.pdb --nequil 10E6 --nprod 50E6</pre>
<p>
you will run 10 m equiliration steps and 50 m production steps (instead of the 5 m and 40 m that is default)
<p>
<h5>Running independent repeats</h5>
Usually it is wise to run sever