Thanks Justin, this is just working amazingly.... ________________________________
From: gmx-users-boun...@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: 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-boun...@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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- ======================================== 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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