Re: Protein moving out of water-box after 10 ns simulation

From: snoze pa (snoze.pa_at_gmail.com)
Date: Fri Feb 29 2008 - 10:55:32 CST

If this is the problem then try to change origin of your protein. move
center of your protein to origin(0,0,0) and then calculate the
cellBasisVector. I also had this problem in past and after moving protein
center coordinates to origin solve this problem.
good luck

On Thu, Feb 28, 2008 at 6:45 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> Nothing is wrong with your simulation. VMD doesn't wrap the molecule
> until more than half of it has crossed the boundary. If you display the
> periodic images of the ions and water, you'll see them around the protein as
> expected.
>
> On Feb 27, 2008, at 10:34 AM, Jie-rong Huang wrote:
>
> Thanks a lot for replying!
>
> I used "wrapAll on", and
> here is the periodic boundary conditions as input
>
> cellBasisVector1 46. 0. 0.
> cellBasisVector2 0. 48. 0.
> cellBasisVector3 0. 0 53.
> cellOrigin 30.841 29.104 18.693
> wrapAll on
>
> Anything is not suitable?
>
> One thing I don't understand is:
> Because periodic boundary conditions is applied, the protein moves out of
> water box should still "in water", it is just not shown in VMD. However,
> those 30 ions I put around protein were all still inside the water box
> instead of surrounding the protein. Does anyone know what happened? Any
> suggestions will be appreciated!!
>
> Best,
>
> Jie-rong
>
>
> 2008/2/27, Per Jr. Greisen <pgreisen_at_gmail.com>:
> >
> > You should probably read the section on wrap-coordinates. That should
> > fix your problem.
> > Hope it helps
> > Best
> >
> > On Wed, Feb 27, 2008 at 3:13 PM, Jie-rong Huang <jierongh_at_googlemail.com>
> > wrote:
> >
> > > Dear NAMD users,
> > >
> > > I run a script (as used in tutorial) with 10 ps minimization and then
> > > run for 10 ns for ubiquitin with 15 Na and 15 Cl randomly added by "Add
> > > Ions" plug-in. However, in the end of 10 ns, part of the protein came out
> > > of the water-bax (I used "solvate" with layer 8A). How I can keep the
> > > protein in the middle of water box during the long trajectory simulation?
> > > Only way I can think about is put
> > >
> > > fixedAtoms on
> > > fixedAtomsForces on
> > > fixedAtomsFile ubiquitin.pdb #column B of a few residue (maybe 1 or
> > > 2) are "1"
> > > fixedAtomsCol B
> > >
> > > However, this "going-out" problem might only be caused by some
> > > parameter setting.....
> > > Can anyone give me some suggestions?
> > >
> > > Jie-rong
> >
> >
> >
>
>

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