[gmx-users] gmx select with coordinates

[Shan Jayasinghe]

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