<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>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 not come at the center:<br><br>1. trjconv -f complete_production.xtc -s test.tpr -o test.pdb -center zero -b 22000<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 translation -b 22000 -o check2.pdb<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">Select group for translational fit<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><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 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 options. <br>Under GMX 3.3.3, there is a -center flag that allows you to select a group for <br>centering. In my protein/membrane systems, it has always worked well (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>> <<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>>
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<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 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
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