AMBER Archive (2007)

Subject: Re: AMBER: question about iwrap

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 11 2007 - 18:24:11 CDT

On Wed, Jul 11, 2007, Kailee wrote:
>
> As said in AMBER manual, set iwrap=1 can wrap the trajectory files into the
> primary box that can make structure more visually but can mess up diffusion
> and other calculations. I am looking at the gas molecule diffusing into a
> protein, and need to look at the gas diffusion pathways, what I want to ask
> is when I look at the diffusion pathways should I reimage the trajectories
> into the primary box or not? as after wrapped into the primary box, the gas
> trajectories are quite different from those before wrapping and become
> incontinuous. I am now a bit confused, which (before or after wrap) states
> are the real situation that I need to do my analysis?

Sounds to me like you want to use the un-wrapped (continuous) trajectories.
Your situation sounds like one where wrapping is not a good idea.

...good luck...dac

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