AMBER Archive (2008)

Subject: Re: AMBER: molecule drift out of water box?

From: Ilyas Yildirim (
Date: Fri Sep 19 2008 - 19:00:03 CDT

Can you try the following in the ptraj imaging?

--------- ------------
.(your trajin files)
.(your trajin files)
.(your trajin files)
image familiar com :(the first res of the protein)-(last res. of the protein)
What this will make is to make sure that the center-of-mass of the protein
will be at the origin. Hope this helps.

PS: I assume that you did not change the box info in the prmtop file.

> I am doing MD for a mouse ubiquitin, 1wgg, which has a long side chain. When
> I solvate the protein, I try solvateoct TIP3PBOX 12.0 and
> solvateoct TIP3PBOX 10.0. And I find out that the size of solute vdw
> bounding box is same: 36.162, 30.853, 52.074. So, I decide to use TIP3PBOX
> 10.0 since it has less water molecules.
> In the amber tutorial, it asks us to reimage all the water molecules into
> the original box. So I did it, and I find out that a very small part of my
> protein side chain drift into the vacuum after 1ns.
> However, if I don't reimage the water molecules into the original box, the
> whole protein is still in water. I am wondering whether or not my protein
> drifts out of water box. Do I trust the reimaged trajectory or the original
> trajectory?
> If my protein do drift out ot the water box, how do I fix it? I think I need
> to enlarge the water box, but both TIP3PBOX 12.0 and TIP3PBOX 10.0 give me
> the same size of water box. I know that if I don't truncate the waterbox, I
> won't have this problem. But I don't want to use so many water molecule in
> the simulation.

  Ilyas Yildirim, Ph.D.
  = Hutchison Hall B#10          - Department of Chemistry      =
  =                              - University of Rochester      =
  = 585-275-6766 (office)        -                              =
  =                     =

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