AMBER Archive (2009)
Subject: [AMBER] Is iwrap mapping water molecules to my protein cavity?
From: ben rodriguez (bramber_at_live.com)
I am looking at internal water molecules in protein cavities, in witch the starting structure contain a water molecule. Periodically, throughout the trajectory, after the water molecule has diffused from the cavity, the original starting water molecule gets reimaged to its starting position inside the cavity. This happened twice as far as I could tell during a 10ns simulation. I looking for this process to occur 'naturally,' not by reimaging water molecules into the cavity.
This was not my understanding of how iwrap behaves? Can any shed some light on this.