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

[Nuno Azoia]

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
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
Nuno Gonçalo Azoia Lopes

Rua Nascente, nº 25
4705-473 Escudeiros

Tel: 253 683 198
Móvel: 965 382 487