[gmx-users] gmx select with coordinates

[Shan Jayasinghe]

Hi Prof. Dan,

Thank you very much  for the e-mail. How do we define coordinates what we
want in VMD Graphical Representation menu?

Thank you.

On Wed, Oct 10, 2018 at 6:53 AM Dan Gil <dan.gil9973 at gmail.com> wrote:

> 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
> > > > --
> > > > Gromacs Users mailing list
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> > --
> > Best Regards
> > Shan Jayasinghe
> > --
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-- 
Best Regards
Shan Jayasinghe