Re: [AMBER] iwrap=1 "can mess up diffusion and other calculations"

From: Charles Lin <>
Date: Wed, 25 Nov 2015 02:56:52 +0000

I believe the manual refers to any post processing you may want to make with your system. I'm not 100% certain about this, I would have to go check the code, but assuming you're running diffusion using COM restraints. You may be getting the wrong distance in DUMPAVE if you turn iwrap=1 because when your molecule moves to the top of the box it comes back in the bottom so you'll not get a true distance but essentially the wrapped distance if you were using center of mass restraints.

If you're doing anything that requires your "real" coordinates and need to post process things it may be better to run iwrap=0 and then post process using cpptraj.

From: Robert Molt []
Sent: Tuesday, November 24, 2015 5:45 PM
To: AMBER Mailing List
Subject: [AMBER] iwrap=1 "can mess up diffusion and other calculations"

The manual states that iwrap=1 "...can mess up...and other
calculations." Can it be specified what these other calculations are?

Dr. Robert Molt Jr.
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Received on Tue Nov 24 2015 - 19:00:03 PST
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