From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Feb 28 2008 - 18:45:54 CST
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!!
> 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
> 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?
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