AMBER Archive (2008)

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

From: Qiuting Hong (qiutinghong_at_gmail.com)
Date: Sun Sep 21 2008 - 20:43:38 CDT

Dear Llyas,

Yes, the reimaged trajectory is different from the one I got before, but
part of the side chain is still outside the water box. I attach
a picture. Do you think I failed in this simulation?
Thank you.

Qiuting Hong

On Sun, Sep 21, 2008 at 1:45 PM, Ilyas Yildirim
<yildirim_at_pas.rochester.edu>wrote:

> 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/ =
> > > ---------------------------------------------------------------
> > >
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
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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/ =
> ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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