[gmx-users] gmx select with coordinates

[Dan Gil]

Hi Shan,

Sorry it's been a while - I don't check this email too often. Did you
figure the problem out?

I use the Graphical Representations menu of VMD, although I am sure there
is a way to do it in the console too.

On Thu, Sep 27, 2018 at 9:35 PM Shan Jayasinghe <
shanjayasinghe2011 at gmail.com> wrote:

> 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
> --
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