urbation, or do the full perturbation in one step. The former can be advantageous if the perturbation is complicated. In addition to create input files for the bound and free leg, the setup will also setup command files for the perturbation in gas-phase. This calculation is of interest if you want to compute relative hydration free energy, or if you want to debug your perturbation. To run the one-step perturbations you need to execute
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<pre>
mpirun -np 16 $PROTOMSHOME/protoms3 run_comb_bnd.cmd
mpirun -np