[gmx-users] gmx select with coordinates
dan.gil9973 at gmail.com
Thu Sep 27 15:59:56 CEST 2018
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
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
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
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
> > 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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