AMBER Archive (2008)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sun Sep 21 2008 - 15:45:45 CDT

Qiuting, try the following:

-------- ptraj_reimage.in-----------
ptraj 1wgg.prmtop << EOF
trajin 1wggmd1.mdcrd
trajin 1wggmd2.mdcrd
trajin 1wggmd3.mdcrd
trajout 1wgg_md_reimaged.mdcrd
image familiar com :1-96
go
------- ptraj.reimage.in---------

On Sun, 21 Sep 2008, Qiuting Hong wrote:

> Dear Llyas,
>
> Thank you for your response. Below is my ptraj file:
> -------- ptraj_reimage.in-----------
> ptraj 1wgg.prmtop << EOF
> trajin 1wggmd1.mdcrd
> trajin 1wggmd2.mdcrd
> trajin 1wggmd3.mdcrd
> trajout 1wgg_md_reimaged.mdcrd
> center :1-96
> image familiar
> go
> EOF
> ------- ptraj.reimage.in---------
>
> Is this what you mean? But when I check the movie of 1wgg_md_reimaged.mdcrd,
> the tip of the side chain dip into the vacuum. I want to know if I need to
> re-run the simulation.
>
> Qiuting Hong
>
>
> On Fri, Sep 19, 2008 at 5:00 PM, Ilyas Yildirim
> <yildirim_at_pas.rochester.edu>wrote:
>
> > Can you try the following in the ptraj imaging?
> > --------- ptraj_imaging.in ------------
> > .(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) - =
> > = http://www.pas.rochester.edu/~yildirim/ =
> > ---------------------------------------------------------------
> >
> > -----------------------------------------------------------------------
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> >
> 

-- 
  Ilyas Yildirim, Ph.D.
  ---------------------------------------------------------------
  = Hutchison Hall B#10          - Department of Chemistry      =
  =                              - University of Rochester      =
  = 585-275-6766 (office)        -                              =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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