[gmx-users] automating analysis using shell scripting

[Justin A. Lemkul]

Hassan Shallal wrote:
> Dear Gromacs users,
>  
> This question is much more of a linux shell scripting than of Gromacs. I have several distances to measure in my produced system for which I use g_dist. I need to shell script this so I don't have to set next to the machine while measuring those distances. The problem I face is that g_dist, and others like g_rms and g_rmsf, asks for input of the number of the group with or without an index file. My question is, how can I use shell scripting to answer those questions given by g_dist, giving it the number of the groups which is usually 0 an 1 using an index file of two atoms in the system?  
>  
> By doing this I can write a shell script of several g_dist lines, each is concerned with a specific distance, the shell script can input the number oif the groups to be measured, and I can do another experiment or go to the gym, or even cook something for dinner until it's done, lol
>  
> Has anyone of you tried doing this?
>  

Yes, see here:

http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive

-Justin

> Thanks alot
> Hassan Shallal
> University of the Pacific
> Stockton, California
> 
> ________________________________
> 
> From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
> Sent: Sat 6/26/2010 8:39 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 143
> 
> 
> 
> 
> 
> lloyd riggs wrote:
>> Dear (Justin too),
>>
>> Thank you for the replies.  My main problem is lack of time, but I still have
>> the end of the proteins problem as of now.
>>
>> I only made the comment to justin partially as a joke, because he A) answeres
>> on averidge about 10-20 of these a day, seems too smart to be a help center,
>> and B) Every freind I have had in the past whom ends up overdoing on the help
>> BB (ie, CCP4, Phsics at CERN, etc...) ends up getting screwed in the end by
>> not balancing the "myself" getting my things done and making connections Vs.
>> Helping everyone else because they know so damned much about a specific
>> topic.  All of my freinds in the similar situation started off looking about
>> as promissing, but then get ragged once they graduate, because everyone seems
>> to want a slave loyal to themselves as a post doc, before the professorship
>> is obtainable, etc...and end up writting video game software, hateing
>> academia for the way it really works Vs. the way it is supposed to work in
>> the scientific ideology we are taught at Universities and highschool.
>>
>> In any case, sorry to you Justin, I didn't mean to be such an ass.
>>
> 
> Apology accepted.  Please don't feel like you have to save me any trouble or
> look out for my productivity.  I only reply to email when I really care to, and
> my comments are intended as helpful, not picky or overly critical :)  I do
> appreciate this follow-up, as I have received several private emails telling me
> I'm a useless jerk, and they really do mean it...
> 
> -Justin
> 
>> Stephan Watkins
>>
> 
> --
> ========================================
> 
> 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
> 
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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

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