lysis for both the electrostatic and van der Waals perturbation. For the gas-phase simulation, you can usually skip analysis of the equilibration, as this leg equilibrates very quickly.

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<h3>Exploring more options</h3>
By running <code>protoms.py</code> as above, you accept the standard number of &lambda;-values, simulation length etc. The values of these parameters were chosen from experience and should work for most systems. However, there are situations when you may want to do s