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

[Dawid das]

Thank you.

2015-09-17 12:37 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> Yes. Further options at
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> Mark
>
> On Thu, Sep 17, 2015 at 1:04 PM Dawid das <addiw7 at googlemail.com> wrote:
>
> > 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?
> > >
> > >
> > --
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