i><code>run_free.cmd</code> = the ProtoMS command file for the free-leg simulation</li>
	<p>
For the single-topology simulations the following files are created:	</p>	
	<li><code>li3-li1_ele.tem</code> = the template file for electrostatic perturbation, used only in this simulation</li>
	<li><code>li3-li1_vdw.tem</code> = the template file for van der Waals perturbation, used only in this simulation</li>
	<li><code>li3-li1_comb.tem</code> = the template file for one-step (combined) perturbation, used only i