[gmx-users] Using shell script to analyze the results

[Kiwoong Kim]

Thanks to Azoia and nayeem

The solution from Azoia is perfectly working :)

Thx.

2012/2/10 Nuno Azoia <nazoia at gmail.com>

> There is a more direct way. In the script just use
>  g_msd -f *.xtc -s *.tpr -o *.xvg -rmcomm <<EOF
>  Number
>  Number
>  EOF
>
> where Number denotes the group number, or the group name, matching the
> definition on the index file. It will work in both ways. It can be
> used with one, two , or the number of "answers" you need to supply.
>
> Nuno Azoia
>
> On Fri, Feb 10, 2012 at 11:54 AM, shahid nayeem <msnayeem at gmail.com>
> wrote:
> > Create a file named input.g_rms. write the group number in this file. In
> > your shell script after command line write <input.g_rms. when the
> command is
> > executed in shell the file input.g_rms having group number will be read.
> > Hope it works.
> > Shahid nayeem
> >
> > On Fri, Feb 10, 2012 at 4:19 PM, Kiwoong Kim <ilmarejoe at gmail.com>
> wrote:
> >>
> >> Hi,
> >>
> >> I'm not good at shell programming now.
> >> For the simplicity, I wrote down all the gromacs commands in one shell
> >> script.
> >>
> >> It means that if I execute the .sh file, then every works including
> graphs
> >> used for analysis are done.
> >> However, when there are g_msd -f *.xtc -s *.tpr -o *.xvg -rmcomm, I have
> >> to select the groups manually.
> >> This is quite inconvenient...
> >>
> >> Is there any way to handle this??
> >>
> >> Thanks in advance
> >>
> >> --
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> >
> >
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>
>
> --
> Nuno Gonçalo Azoia Lopes
>
> Rua Nascente, nº 25
> 4705-473 Escudeiros
>
> Tel: 253 683 198
> Móvel: 965 382 487
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