Hi Aniko, Another option is to use a HERE doc such as:
gmx something << HERE 0 1 HERE which would execute the gmx command and give it as input: 0, a return character, and then 1 (with a return character also). Check the advanced bash-scripting guide for more details: http://tldp.org/LDP/abs/html/here-docs.html -Micholas =================== Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: [email protected] <[email protected]> on behalf of Kutzner, Carsten <[email protected]> Sent: Friday, July 31, 2015 5:13 AM To: [email protected] Subject: Re: [gmx-users] submitting gmx cluster Hi Aniko, > On 31 Jul 2015, at 10:52, Lábas Anikó <[email protected]> wrote: > > Dear Gromacs Users, > > I would like to submit my 'gmx cluster' job, but I don't know how can I > define in my command line the following two options, which normally appear > on the screen when I run gmx cluster on my head machine: > 1. "Select group for least squares fit and RMSD calculation" > 2. "Select group for output" > > Can You tell me any suggestions? You can pipe in your selections using echo in bash: echo “0” | gmx something … The above one would simply pass “0” to gmx something. For multiple choices including returns you can do something like echo “0\n 14\n” | gmx … This would select 0 and 14, followed by a return “\n”. Carsten > > Thank You in advance! > > Aniko > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
