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

From: Jason Swails <>
Date: Tue, 24 Nov 2015 23:57:26 -0500

On Tue, Nov 24, 2015 at 9:56 PM, Charles Lin <> wrote:

> 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.

​Good advice. The only addition I'll make is that if you use iwrap=0, you
should *also* use ntxo=2 and ioutfm=1 to write coordinate files to NetCDF
format (this avoids overflowing the ASCII formats and ending up with
useless coordinate or trajectory files).

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 24 2015 - 21:00:04 PST
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