<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div>You are right, I am using 3.3, sorry for this mistake. I will try the command which you have mentioned with -center zero for a small number of frames i.e. -b 2000 -e 3000 and get back to you. <br><br>thnx,<br>Pri...<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;">----- Original Message ----<br>From: Justin A. Lemkul <jalemkul@vt.edu><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Tuesday, 12 August, 2008 1:15:00 AM<br>Subject: Re: [gmx-users] translation<br><br><br><br>priyanka srivastava wrote:<br>> Dear Justin,<br>> <br>> Thanks a lot for replying back.<br>> <br>> These are the two things that I have tried but still the
peptide does <br>> not come at the center:<br>> <br>> 1. trjconv -f complete_production.xtc -s test.tpr -o test.pdb -center <br>> zero -b 22000<br><br>The "-center zero" flag is not an option in 3.3.3, are you sure these are the <br>commands you gave, and you are using the version you think you are?<br><br>I'm thinking that there is too big of a difference from 0 to 22 ns to allow <br>trjconv accurately apply the fix.<br><br>Try this:<br><br>trjconv -f complete_production.xtc -s test.tpr -center<br><br>As a basic test, it should re-center your chosen group (Protein) every frame, <br>allowing an iterative fix of the motion.<br><br>> Select group for centering<br>> Protein<br>> <br>> Select group for output<br>> System<br>> <br>> 2. trjconv -f complete_production.xtc -s test.tpr -center zero -fit <br>> translation -b 22000 -o check2.pdb<br>> Select group for translational fit<br><br>Same comments as a above, if you
don't process every frame (or at least a <br>reasonably spaced subset), the algorithm doesn't tend to give the desired <br>output, or so I have noticed with -center and -pbc options.<br><br>-Justin<br><br>> Selected 0: 'System'<br>> <br>> Select group for centering<br>> Selected 1: 'Protein'<br>> <br>> Select group for output<br>> System<br>> <br>> I am using 3.3.3.<br>> <br>> thnx,<br>> Priyanka..<br>> <br>> <br>> ----- Original Message ----<br>> From: Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Tuesday, 12 August, 2008 12:05:26 AM<br>> Subject: Re: [gmx-users] translation<br>> <br>> <br>> <br>> priyanka srivastava wrote:<br>> > Dear
All,<br>> ><br>> > I really apologize for asking a peptide translation related question<br>> > again. I have a lipid-peptide system and I have already carried out the<br>> > production run for 20ns. The peptide has moved towards one of the edges<br>> > (I didnt specify comm-grps in the mdp file). I have to translate the<br>> > peptide in the center of the bilayer. While using trjconv it translates<br>> > the peptide at 0,0,0 but shifts the lipid and water molecules as well<br>> > such that eventually the peptide lies near the edge only!<br>> <br>> Without seeing what command you've actually tried, it's hard to make any<br>> recommendation.<br>> <br>> > Is there any other tool which I should be using?<br>> <br>> trjconv is the tool you want, it's just a matter of finding the right <br>> options.<br>> Under GMX 3.3.3, there
is a -center flag that allows you to select a <br>> group for<br>> centering. In my protein/membrane systems, it has always worked well <br>> (choose<br>> Protein for the group to be centered).<br>> <br>> -Justin<br>> <br>> > Kindly suggest me something,<br>> > Priyanka.<br>> ><br>> > ------------------------------------------------------------------------<br>> > Bollywood news, movie reviews, film trailers and more! Click here.<br>> > <br>> <<a href="http://in.rd.yahoo.com/tagline_movies_1/*http://in.movies.yahoo.com/?wm=n/" target="_blank">http://in.rd.yahoo.com/tagline_movies_1/*http://in.movies.yahoo.com/?wm=n/</a>><br>> ><br>> ><br>> > ------------------------------------------------------------------------<br>> ><br>> > _______________________________________________<br>>
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href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> > Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <br>> <mailto:<a
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------------------------------------------------------------------------<br>> Be the first one to try the new Messenger 9 Beta! Click here. <br>> <<a href="http://in.rd.yahoo.com/tagline_messenger_7/*http://in.messenger.yahoo.com/win/" target="_blank">http://in.rd.yahoo.com/tagline_messenger_7/*http://in.messenger.yahoo.com/win/</a>><br>> <br>> <br>> ------------------------------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>> Please don't post
(un)subscribe requests to the list. Use the <br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a
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