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 <msnay...@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 <ilmare...@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@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list gmx-users@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-requ...@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 -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists