r"/>
<h3>Simple setup &mdash; dual-topology simulation</h3>
<h5>Setup</h5>
The simplest way to setup the simulation is by typing the following
<p>
<pre>python $PROTOMSHOME/protoms.py -s dualtopology -l lig1.pdb lig3.pdb -p protein.pdb</pre>
<p>
this sets up one simulation for the bound leg and one for the free leg of the relative free energy cycle.<p> The simulations will run 5 m equilibration steps and 40 m production steps for each of the 16 &lambda;-values. Output will be printed to files every 100 k mov