  The process of ligand-protein unbinding is crucial in biophysics. Water is an
essential part of any biological system and yet, many aspects of its role
remain elusive. Here, we simulate with state-of-the-art enhanced sampling
techniques the binding of Benzamidine to Trypsin which is a much studied and
paradigmatic ligand-protein system. We use machine learning methods to
determine efficient collective coordinates for the complex non-local network of
water. These coordinates are used to perform On-the-fly Probability Enhanced
Sampling simulations, which we adapt to calculate also the ligand residence
time. Our results, both static and dynamic, are in good agreement with
experiments. We find that the presence of a water molecule located at the
bottom of the binding pocket allows via a network of hydrogen bonds the ligand
to be released into the solution. On a finer scale, even when unbinding is
allowed, another water molecule further modulates the exit time.
