es and Hamiltonian replica-exchanges between neighbouring &lambda;-values will be attempted every 100 k moves.  
<p>
the <code>-s dualtopology</code> argument tells the script to setup a dual topology free energy simulation and the <code>-p</code> and <code>-l</code> arguments specify the protein and the ligands respectively.
<p> 
You can read more about the files that the setup script creates further down on this <a href="#files">page</a>.
<p>You can visualise the systems that will be simulated with (for i