Re: AMBER: question about iwrap

From: Carlos Simmerling <>
Date: Thu, 12 Jul 2007 07:34:08 -0400

they won't be inside the protein. when you use wrapping, when a molecule
leaves the central unit cell it is removed and translated to where the
periodic image of that molecule entered the unit cell. with wrapping off,
you always track the same molecule even when it leaves the unit cell.
both are the same physically, since it is a periodic system the periodic
images of the molecules "exist" in the simulation. the only change is which
images of the molecule are written to the file. all of them are present in
the simulation.

taking a look at some of the images of periodic systems might help, you can do
a gogole search for "periodic boundary conditions" and click on images.
for example, CCL has a good explanation:

On 7/12/07, Kailee <> wrote:
> 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,
> Kailee
> 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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