n this simulation</li>
	<li><code>single_cmap.dat</code> = the atom correspondence map</li>
	<li><code>run_comb_bnd.cmd</code>, <code>run_ele_bnd.cmd</code> and <code>run_vdw_bnd.cmd</code> = the ProtoMS command files for the bound-leg simulation</li>
	<li><code>run_comb_free.cmd</code>, <code>run_ele_free.cmd</code> and <code>run_vdw_free.cmd</code> = the ProtoMS command file for the free-leg simulation</li>
	<li><code>run_comb_gas.cmd</code>, <code>run_ele_gas.cmd</code> and <code>run_vdw_gas.cmd</code> =