This might be the solution.
Thank you,
Stephen
________________________________
From: Timothy Giese <giese025.rutgers.edu>
Sent: Thursday, March 5, 2026 2:38 PM
To: Slimak, Stephen Rudolph <SRS215.pitt.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Imaging question
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If I am understanding correctly, then for your application it sounds like you should consider setting iwrap=0 so the coordinates are not imaged when amber writes the restart and trajectory files so your calculations can be run more easily and avoid breaking your restraints. By setting iwrap=0, the primary unit cell will look like the solvent is evaporating, but it's totally fine when considering periodicity. You can always later go back and image the system to make a "clean looking" unit cell to prepare figures and presentations. But the point of setting iwrap=0 is to prevent multiple solute molecules from imaging to opposite sides of the unit cell when applying restraints that don't consider periodicity. -Tim
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Received on Thu Mar 05 2026 - 15:30:02 PST
