[gmx-users] automating analysis using shell scripting
hshallal at PACIFIC.EDU
Wed Jun 30 03:24:01 CEST 2010
Thanks Justin, this is just working amazingly....
From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
Sent: Tue 6/29/2010 6:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] automating analysis using shell scripting
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:
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
gmx-users mailing list gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before posting!
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