[gmx-users] automating analysis using shell scripting

Hassan Shallal hshallal at PACIFIC.EDU
Wed Jun 30 03:08:27 CEST 2010

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?
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...


> Stephan Watkins


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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