al independent repeats of your calculation to check for convergence. The argument that controls the number of independent repeats is called <code>--repeats</code> or just <code>-r</code>.
<p>
by typing for instance
<p>
<pre>python $PROTOMSHOME/protoms.py -s jaws1 -p protein.pdb -l fragment.pdb -r 5</pre>
<p>
you will create 5 input files for the JAWS calculation. Therefore, you also need to execute ProtoMS 5 times with the different input files. The output will be in 5 different folders, e.g. <code>out1_jaw