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

From: Jason Swails <>
Date: Tue, 24 Nov 2015 21:57:12 -0500

On Tue, Nov 24, 2015 at 8:45 PM, Robert Molt <> wrote:

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

​Diffusion and diffusion-related calculations. Anything that depends on
tracking a *particular* particle's trajectory​ through time will be messed
up by imaging/iwrap=1 (since the coordinates specified for a particular
atom may change from one image to another during the course of the

However, assuming you have a continuous time series of trajectory files,
the "unwrap" command in cpptraj will reverse the effects of "iwrap=1" and
allow you to perform these kinds of calculations.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 24 2015 - 19:00:04 PST
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