[gmx-users] gmx select with coordinates

[Dan Gil]

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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