<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">Thanks it worked!<br><br>I useed trjconv to create a new .xtc just with the backbone and now I can do a g_rms for both simulations.<br><br>Cheers<br><br>Afonso<br><br><br><br><br>Today's Topics:<br><br> 1. Re: RMSD of the same protein in different solvent boxes<br> (Tsjerk Wassenaar)<br> 2. Re: RMSD of the same protein in different solvent boxes<br> (Florian Haberl)<br> 3. Re: RMSD of the same protein in different solvent boxes<br> (Ran Friedman)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Mon, 5 Feb 2007 11:22:23 +0100<br>From: "Tsjerk Wassenaar" <tsjerkw@gmail.com><br>Subject: Re: [gmx-users] RMSD of the same protein in different solvent<br> boxes<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Message-ID:<br>
<8ff898150702050222v5e26a791v74a4ebacdd62bae7@mail.gmail.com><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Hi Afonso,<br><br>Try to first extract the protein from both simulations using trjconv,<br>or even the backbone trajectories.<br><br>Cheers,<br><br>Tsjerk<br><br>On 2/5/07, Afonso Duarte <duartenl@yahoo.com.br> wrote:<br>> Hi to All,<br>><br>> I have some simulations of the same protein in different solvents, with<br>> different number of atoms for each (different solvent number of atoms).<br>> I would like to calculate a rmsd matrix to compar the backbone of the<br>> different sims.<br>><br>> I have tried g_rms with the -f2 option to include the second trajectory,<br>> however it finishes with a fatal error because teh number of total atoms is<br>> different in both trajectories.<br>><br>> Does anybody know how to solve this question? Is it possible to produce the<br>> rmsd matrix in a different
way?<br>><br>> Thanks in advance<br>><br>> Afonso<br>><br>><br>> __________________________________________________<br>> Fale com seus amigos de graça com o novo Yahoo! Messenger<br>> http://br.messenger.yahoo.com/<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read<br>> http://www.gromacs.org/mailing_lists/users.php<br>><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<br><br><br>------------------------------<br><br>Message: 2<br>Date: Mon, 5 Feb 2007 11:31:27 +0100<br>From: Florian Haberl
<Florian.Haberl@chemie.uni-erlangen.de><br>Subject: Re: [gmx-users] RMSD of the same protein in different solvent<br> boxes<br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Message-ID: <200702051131.28088.Florian.Haberl@chemie.uni-erlangen.de><br>Content-Type: text/plain; charset="utf-8"<br><br>hi,<br><br>On Monday, 5. February 2007 11:13, Afonso Duarte wrote:<br>> Hi to All,<br>><br>> I have some simulations of the same protein in different solvents, with<br>> different number of atoms for each (different solvent number of atoms). I<br>> would like to calculate a rmsd matrix to compar the backbone of the<br>> different sims.<br>><br>> I have tried g_rms with the -f2 option to include the second trajectory,<br>> however it finishes with a fatal error because teh number of total atoms is<br>> different in both trajectories.<br>><br>> Does anybody know how to solve this question? Is it possible to produce
the<br>> rmsd matrix in a different way?<br><br>reduce both simulations to matching atomsize, e.g. for both simulations:<br>make_ndx (only backbone atoms) <br><br>trjconv ..<br><br>g_rms <br><br>><br>> Thanks in advance<br>><br>> Afonso<br>><br>> __________________________________________________<br>> Fale com seus amigos de graça com o novo Yahoo! Messenger<br>> http://br.messenger.yahoo.com/<br><br>greetings,<br><br>Florian<br><br>-- <br>-------------------------------------------------------------------------------<br> Florian Haberl <br> Computer-Chemie-Centrum <br> Universitaet Erlangen/ Nuernberg<br> Naegelsbachstr 25<br> D-91052 Erlangen<br> Telephone: +49(0) − 9131 − 85 26581<br> Mailto: florian.haberl AT chemie.uni-erlangen.de<br>-------------------------------------------------------------------------------<br><br><br>------------------------------<br><br>Message: 3<br>Date: Mon, 05 Feb 2007 11:22:55
+0100<br>From: Ran Friedman <r.friedman@bioc.unizh.ch><br>Subject: Re: [gmx-users] RMSD of the same protein in different solvent<br> boxes<br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Message-ID: <45C7057F.6050600@bioc.unizh.ch><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi,<br><br>If it's the same protein you can extract the trajectories with the<br>coordinates of the protein only using trjconv.<br><br>Ran.<br><br>Afonso Duarte wrote:<br>> Hi to All,<br>><br>> I have some simulations of the same protein in different solvents,<br>> with different number of atoms for each (different solvent number of<br>> atoms).<br>> I would like to calculate a rmsd matrix to compar the backbone of the<br>> different sims.<br>><br>> I have tried g_rms with the -f2 option to include the second<br>> trajectory, however it finishes with a fatal error because teh number<br>> of total atoms is different in both
trajectories.<br>><br>> Does anybody know how to solve this question? Is it possible to<br>> produce the rmsd matrix in a different way?<br>><br>> Thanks in advance<br>><br>> Afonso<br>><br>> __________________________________________________<br>> Fale com seus amigos de graça com o novo Yahoo! Messenger<br>> http://br.messenger.yahoo.com/<br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br><br>-- <br>------------------------------------------------------<br>Ran Friedman<br>Postdoctoral Fellow<br>Computational
Structural Biology Group (A. Caflisch)<br>Department of Biochemistry<br>University of Zurich<br>Winterthurerstrasse 190<br>CH-8057 Zurich, Switzerland<br>Tel. +41-44-6355593<br>Email: r.friedman@bioc.unizh.ch<br>Skype: ran.friedman<br>------------------------------------------------------<br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20070205/d379e97b/attachment-0001.html<br><br>------------------------------<br><br>_______________________________________________<br>gmx-users mailing list<br>gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br><br><br>End of gmx-users Digest, Vol 34, Issue
8<br>****************************************<br></gmx-users@gromacs.org></r.friedman@bioc.unizh.ch></gmx-users@gromacs.org></Florian.Haberl@chemie.uni-erlangen.de></duartenl@yahoo.com.br></gmx-users@gromacs.org></tsjerkw@gmail.com></blockquote><br><p> __________________________________________________<br>Fale com seus amigos de graça com o novo Yahoo! Messenger <br>http://br.messenger.yahoo.com/