ualize the positions of the waters at one given point in the simulation, for example, at the middle of your production run, type:
<pre>
vmd snapshot_200.pdb
</pre>
and try to see if there was any water in the binding site (the residue name of your jaws waters is "WA1"). Remember that whichever JAWS waters you may find, are the "on" &mdash; fully interacting &mdash; waters (with &#952; > 0.95, where &#952; corresponds to the scaling of their interactions).
But looking at each snapshot individually is hard to