[gmx-users] Choose index group from terminal input.
mark.j.abraham at gmail.com
Thu Sep 17 13:37:34 CEST 2015
Yes. Further options at
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:
> 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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