[gmx-users] submitting gmx cluster

[Smith, Micholas D.]

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: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kutzner, Carsten <ckutzne at gwdg.de>
Sent: Friday, July 31, 2015 5:13 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] submitting gmx cluster

Hi Aniko,

> On 31 Jul 2015, at 10:52, Lábas Anikó <labasaniko at gmail.com> 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
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--
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

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