[gmx-users] Choose index group from terminal input.

[Dawid das]

O'right, I have figured that out myself. Just use text file like data.txt
with two lines:
1
1

and redirect it: g_rms [options] < data.txt

2015-09-17 11:32 GMT+01:00 Dawid das <addiw7 at googlemail.com>:

> Dear Gromacs Experts,
>
> Let's say that for some reasons I don't want to specify the atom group
> when g_rms (or other module) prompts me to do so.
> So I do not want to see this:
>
> Select group for RMSD calculation
> Group     0 (         System) has 38387 elements
> Group     1 (        Protein) has  3470 elements
> Group     2 (      Protein-H) has  1772 elements
> Group     3 (        C-alpha) has   217 elements
> Group     4 (       Backbone) has   653 elements
> Group     5 (      MainChain) has   869 elements
> Group     6 (   MainChain+Cb) has  1065 elements
> Group     7 (    MainChain+H) has  1076 elements
> Group     8 (      SideChain) has  2394 elements
> Group     9 (    SideChain-H) has   903 elements
> Group    10 (    Prot-Masses) has  3461 elements
> Group    11 (    non-Protein) has 34917 elements
> Group    12 (          Water) has 34845 elements
> Group    13 (            SOL) has 34845 elements
> Group    14 (      non-Water) has  3542 elements
> Group    15 (            Ion) has    72 elements
> Group    16 (             NA) has    37 elements
> Group    17 (             CL) has    35 elements
> Group    18 ( Water_and_ions) has 34917 elements
> Group    19 (    Chromophore) has    37 elements
> Select a group: 1
> Selected 1: 'Protein'
>
> and I want to specify this Group 1 (Protein) in my command, e.g.
> g_rms -s ../npt-md2.tpr -f ../npt-md2.xtc -tu ns -b 0 -e 100 -n
> ../index.ndx -o rmsd-0-100.xvg
> -some_option 1
> Is it possible?
>
>