Running independent repeats</h5>
Usually it is wise to run several independent repeats of your calculation to check for convergence and to obtain a good estimate of the statistical uncertainty. The argument that controls the number of independent repeats is called <code>--repeats</code> or just <code>-r</code>.
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by typing for instance
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<pre>python $PROTOMSHOME/protoms.py -s dualtopology -l lig1.pdb lig3.pdb -p protein.pdb -r 5</pre>
you will create 5 input files for the bound leg and 5 input files for