 16 $PROTOMSHOME/protoms3 run_comb_free.cmd
mpirun -np 16 $PROTOMSHOME/protoms3 run_comb_gas.cmd
</pre>
<p>

This is most conveniently done on a computer cluster. The calculations will take approximately 48 h to complete.
<p></p>
<h5>Analysis</h5>
When the simulations are finished you need to analyse the simulation and extract the free energy of the bound and free legs. This procedure is the same as for the dual-topology simulation as above. If you decide to split up the perturbation, you need to do the ana