[gmx-users] non interactive command

[Justin A. Lemkul]

aiswarya pawar wrote:
> i have N number of selection ie it should run as a batch. like its 
> should select group1: 0 and select group2: 32, this is 1st run then 
> after this next run should be  select group1: 1 and select group2: 32 
> and so on.
> 

So enclose the call to the program in a for-loop in a script, echoing variables 
as necessary.

-Justin

> On Wed, Sep 28, 2011 at 10:56 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     aiswarya pawar wrote:
> 
>         justin,
> 
>         if i use echo command then i need to run again and again for
>         each selection right? how can i run as whole bunch.
> 
> 
>     I don't understand your question.  You can write a trivial shell
>     script for all of your analysis, e.g.:
> 
>     #!/bin/bash
> 
>     echo 4 4 | g_rms -f traj.xtc -s topol.tpr
> 
>     echo 1 | g_gyrate -f traj.xtc -s topol.tpr
> 
>     (etc)
> 
>     -Justin
> 
>         Thanks
> 
> 
>         On Wed, Sep 28, 2011 at 10:31 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            aiswarya pawar wrote:
> 
>                Hi users,
> 
>                I have n number of program to run so my index file is huge, i
>                want to know if i use the command option g_energy -flags <
>                choice.txt , it takes up the numbers given right? but if
>         i have
>                n numbers in the choice txt. how would it take in each
>         run , ie
>                it will take 1st two numbers and what about the rest?
> 
> 
>            You should only provide the chosen number(s), otherwise the
>         program
>            will try to read all of them.  In the case where you have many
>            different programs to run, it is vastly easier to run, for
>         instance:
> 
>            echo x y | g_program -flags
> 
>            -Justin
> 
>            --     ==============================____==========
> 
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
>         <http://vt.edu/Pages/Personal/justin>
>            <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
> 
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> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================