[gmx-users] Help with gmx make_ndx

[Mark Abraham]

Hi,

What do you think is wrong about the contents of the index group that was
made?

Mark

On Tue, Aug 23, 2016 at 6:26 PM Quyen V. Vu <vuqv.phys at gmail.com> wrote:

> Dear gromacs user,
> my system contain such groups:
>
>   0 System              : 943920 atoms
>   1 DNA                 :  3198 atoms
>   2 LA                  :    76 atoms
>   3 CL                  :   130 atoms
>   4 Water               : 940516 atoms
>   5 SOL                 : 940516 atoms
>   6 non-Water           :  3404 atoms
>   7 Other               :    76 atoms
>   8 LA                  :    76 atoms
>   9 CL                  :   130 atoms
>  10 Ion                 :   130 atoms
>  11 LA                  :    76 atoms
>  12 CL                  :   130 atoms
>  13 Water_and_ions      : 940646 atoms
>
> Now, I want to get index of La and CL ions then I type:
>        gmx make_ndx -f em.gro -o index.ndx
> at the make_ndx prompt I type: "8|9"
> then in my index.ndx I get group [LA_CL], also get [system] group ( too
> much index)
> How can I use correct make_ndx?
> Thank you.
> --
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