[gmx-users] gmx select with coordinates

[Shan Jayasinghe]

Dear Prof. Dan,

Thank you very much for the suggestion. However, when I gave the command;
gmx select -f run05.xtc -s run05.tpr -b 390000 -e 400000 -on index.ndx in
VMD TkConsole, I didn't get any output.

I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90
and y. What could be the reason for this? Appreciate, if you can reply me.

Thank you.

On Fri, Sep 28, 2018 at 12:00 AM Dan Gil <dan.gil9973 at gmail.com> wrote:

> Hi,
>
> I believe you are trying to select atoms/particles that are in an
> infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and
> (90, 125)?
>
> Gmx select uses commands that are similar in syntax to a software called
> VMD. So I like to use VMD to figure out what I need to give to gmx select
> in order to get the selections I want.
>
> For example, I think for what you want, I would do:
>
> gmx select -f run05.xtc -s run05.tpr -b 390000 -e 400000 -on index.ndx
> [Press Enter]
> x > 45 and x < 90 and y > 90 and y < 125 [Press Enter]
>
> If you want to include it in a script without manual user input:
>
> echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc -s
> run05.tpr -b 390000 -e 400000 -on index.ndx
>
> VMD is great! It's also free software if you haven't tried using it yet.
> The only thing you gotta watch out for is that VMD uses Angstroms while GMX
> uses nm.
>
> Dan
>
> On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe <
> shanjayasinghe2011 at gmail.com> wrote:
>
> > Dear Gromacs users,
> >
> > I want to make an index files with molecules in a particular area. I have
> > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which
> > define an area of the system. How can I do it with gmx_select?
> >
> > Can anyone help me?
> >
> > Thank you.
> >
> > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe <
> > shanjayasinghe2011 at gmail.com> wrote:
> >
> > >
> > > Dear Gromacs users,
> > >
> > > I want to make an index files with particular x and y coordinates.
> There
> > > is no restriction for z coordinates. How can I do it with gmx_select? I
> > > already tried with the following command. However, it seems I don't get
> > the
> > > result I want.
> > >
> > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f
> > > run05.xtc -s run05.tpr -b 390000 -e 400000 -on index.ndx
> > >
> > > Can anyone help me?
> > >
> > > Thank you.
> > >
> >
> >
> > --
> > Best Regards
> > Shan Jayasinghe
> > --
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-- 
Best Regards
Shan Jayasinghe