he bound leg and 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 moves and Hamiltonian replica-exchanges between neighbouring &lambda;-values will be attempted every 100 k moves.  
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<h5>Execution</h5>
The setup above will produce several ProtoMS command files. You have a choice to split up the perturbation in an electrostatic and van der Waals pert