What you see here is a void in the box.
You need to relax your system with NPT simulation first before you start to
run NVT simulation.
On Wed, Aug 31, 2011 at 4:32 PM, Sai Kumar Ramadugu <sramadugu.gmail.com>wrote:
> Hi Dr. Cheatum,
> Thanks for the reply and suggestions.
> My ligand is a disaccharide. According to GLYCAM naming conventions the
> disaccharide has three residues, so my ligand is from residues 52-54.
> I did the centering and imaging for 1-51 residues. The water box appears
> weird.
> I'm attaching the pdf of the box.
> I'm running an NVT simulation. The attached pdf is the first snapshot of
> the
> system.
> I'm pasting my NVT md input file. Do you think that the simulation has some
> intrinsic problems?
> -----
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 5,
> ntb = 1,
> cut = 10.0,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> temp0 = 300.0,
> ig = -1,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 5000000, dt = 0.002
> ntpr = 10000, ntwx = 25000, ntwr = 25000
> /
> -------------
>
> Sorry if these are to naive questions.
>
>
> Regards
> Sai
>
> On Thu, Aug 25, 2011 at 5:06 PM, Thomas Cheatham III <tec3.utah.edu>
> wrote:
>
> >
> > > I have a system with a protein bound by a ligand non-covalently.
> > > After running the NVT simulation for 10ns, I was trying to image the
> > system
> > > to wrap the water molecules, but I could not.
> > > The sets of commands I used
> > >
> > > I. center :1-54 mass origin
> > > image origin center
> >
> > OK, that centers residues 1-54 to the origin, and images around the
> > origin using the center of mass of each molecule. All molecules center
> of
> > masses WILL be inside the periodic box unless there is some error in the
> > imaging which is unlikely.
> >
> > > II. center :1-54 mass origin
> > > image origin center triclinic
> >
> > The same, except that the triclinic box shape will be observed.
> >
> > > III. center mass origin
> > > image origin center
> >
> > This centers either nothing or everything, followed by imaging.
> >
> > > I was reading earlier posts by various members of the community but
> still
> > > could not solve the issue. The issue is, not all the water molecules
> are
> > > wrapped back into the box. Some water molecules still appear outside
> the
> > > box.
> >
> > All of these methods should put all of the waters into the periodic box.
> > Whether solute is in the box will depend on the centering, i.e. parts of
> > it may appear outside the box (with a hole in the water on the other side
> > where the solute outside the box periodically should be).
> >
> > If residues 1:54 include the ligand, do instead
> >
> > center :1-53 mass origin
> > image origin center
> >
> > However, regardless, are you sure waters are outside the box? If you
> > happened to not have run constant pressure you could have vacuum bubbles
> > (which might make it look like molecules are outside the box). Some
> > visualization programs can display the periodic box boundaries or you can
> > create a PDB file that puts "atoms" at the box vertices and use CONECT
> > records to draw the box lines.
> >
> > --tec3
> >
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> >
>
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--
Best,
InSuk Joung
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Received on Wed Aug 31 2011 - 14:00:04 PDT
