Re: AMBER: question about iwrap

From: Kailee <>
Date: Thu, 12 Jul 2007 11:55:28 +0100

Hi, David,

Thank you for your reply.

Can anyone tell me more about the differences between the wrapped and
unwrapped states please? from my results, gas molecules that are outside the
protein if unwrapped may become inside the protein when the trajectory is
wrapped into the primary box, therefore the results could be obtained will
be totally different. I really want to know which states indicate the real
situation. Thank you.

Best regards,

On 7/12/07, David A. Case <> wrote:
> 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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Received on Sun Jul 15 2007 - 06:07:22 PDT
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