[gmx-users] Zn moves away from protein - ligand complex

[Mark Abraham]

Hi,

The operations you are doing are working differently on the different
ranges of values that the various groups take over the course of the
simulation. The only way to get a reliable result in all cases is to
actually say what you want - that these three things belong always
together.

Mark

On Tue, 19 Apr 2016 01:55 HongTham <hongtham0709 at gmail.com> wrote:

> HI Mark,
> I don't get the reason why this happens to Zn since Protein and ligand are
> fix well with trjconv options.
> Would you please point to me particular reason for it? is it simply because
> of visualization or there is really problem with simulation?
>
> Thank you very much
> Hongtham
>
> On Mon, Apr 18, 2016 at 9:35 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > If you have a cluster of things that make sense to treat together then
> you
> > must tell the tool that, via using such an index group. We haven't yet
> > worked out to implement "do what I want" :-)
> >
> > Mark
> >
> > On Mon, 18 Apr 2016 13:40 HongTham <hongtham0709 at gmail.com> wrote:
> >
> > > Hello Gromacs users,
> > > I'm running a Zn bound protein - ligand complex simulation. I solvated
> > > whole system in a dodecahedron box. I also meet the problems with
> > boundary
> > > effects. I try to use the gmx trjconv with option -pbc mol -ur compact
> > > -center to fix the problem. However, it doesn't work. The protein and
> > > ligand was centered to the water box, but not Zn ion.
> > > In some frame, Zn stay in the active site, sometime, it appear out site
> > of
> > > the active site. I use VMD and display the system with many box (not
> only
> > > one unit), and see ZN till stay in the active site, but that is Zn of
> > > neighbor box, not the current box. its Zn ion now is stay in the active
> > > site of another box.
> > > I also tried with many option (cluster, nojump, -fit rot+trans) or
> change
> > > the selection of centering but they all useless. The -pbc nojump seems
> to
> > > be fine , it makes the protein + ligand + Zn stay together, but the
> water
> > > molecules are definitely distracted. It is difficult for me to
> calculate
> > > the water molecules within 0.5 to 10 nm of Zn and ligand.
> > > Anyone has been same situation with me? Would anyone give me a
> suggestion
> > > to fix that problem.
> > > Thank you so much.
> > > Best regards,
> > > Hongtham
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>