<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Create an index file with (at least) two groups. One group will be used for fitting the structures (e.g. Calpha atoms), and the other for analysis (e.g. your single atom or residue).</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Provide this index file to g_rms, select the first group when asked for the fitting group, and the second as the group to calculate cRMS/RMSD for.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The fitting is an integral part when calculating RMSD. If you fit a single atom the RMSD will always be 0.0, and if you fit a residue the RMSD will only cover internal fluctuations in that residue. Only you can determine what you really want to fit to.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>You might want to take a look at the program g_rmsf too, which calculates the average amount of fluctuations for atoms, either around the starting state (default), or around an average structure you can determine e.g. with g_traj.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On Oct 17, 2006, at 6:01 PM, Viswanadham Sridhara wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">May be you can build an index file which has that specific residue or atom and use it.<BR>If not, definitely you can make trajectory with that single atom/ residue and then use g_rmsd to get what you want.<BR><BR>I hope its clear. <BR><BR><DIV><SPAN class="gmail_quote">On 10/17/06, <B class="gmail_sendername">Guenter Fritz</B> <<A href="mailto:guenter.fritz@uni-konstanz.de">guenter.fritz@uni-konstanz.de</A>> wrote:</SPAN><BLOCKQUOTE class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Dear Viswanadham,<BR><BR>I used g_rmsd but did not find out how to select a single atom or<BR>residue. I just got as far as the pre-defined groups in g_rmsd (groups<BR>1-14).<BR>Is there something like a a "sub-option" ? <BR><BR>> You mean you dint find g_rmsd subroutine or you dint know the way to<BR>> use g_rmsd?<BR>><BR>> On 10/17/06, *Guenter Fritz* < <A href="mailto:guenter.fritz@uni-konstanz.de">guenter.fritz@uni-konstanz.de </A><BR>> <mailto:<A href="mailto:guenter.fritz@uni-konstanz.de">guenter.fritz@uni-konstanz.de</A>>> wrote:<BR>><BR>> Dear all,<BR>><BR>> I want to extrat a rmsd of a single atom or specific residue from <BR>> the<BR>> md trajectory. Should be simple but I didn't dind it.<BR>> Thanks,<BR>> Guenter<BR>><BR>><BR>> _______________________________________________<BR>> gmx-users mailing list <A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <mailto:<A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>> <A href="http://www.gromacs.org/mailman/listinfo/gmx-users"> http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>> Please don't post (un)subscribe requests to the list. Use the<BR>> www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org </A><BR>> <mailto:<A 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">http://www.gromacs.org/mailing_lists/users.php </A><BR>><BR>><BR>><BR>><BR>> --<BR>> Viswanadham Sridhara,<BR>> Research Assistant,<BR>> Old Dominion University,<BR>> Norfolk, Va-23529.<BR>><BR>>------------------------------------------------------------------------ <BR>><BR>>_______________________________________________<BR>>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>><A href="http://www.gromacs.org/mailman/listinfo/gmx-users"> http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>>Please don't post (un)subscribe requests to the list. Use the<BR>>www interface or send it to <A 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">http://www.gromacs.org/mailing_lists/users.php</A><BR>><BR><BR><BR>--<BR>***********************************<BR><BR>Dr. Guenter Fritz <BR>Fachbereich Biologie<BR>Sektion Naturwissenschaften<BR>Universitaet Konstanz<BR><BR>Universitaetsstrasse 10<BR>Postfach M665<BR>D-78457 Konstanz<BR><BR>e-mail: <A href="mailto:Guenter.Fritz@uni-konstanz.de">Guenter.Fritz@uni-konstanz.de </A><BR><BR>http:\\<A href="http://www.biologie.uni-konstanz.de">www.biologie.uni-konstanz.de</A>\fritz<BR><BR>Tel.: +49-(0)7531 88 3687<BR>Fax: +49-(0)7531 88 2966<BR><BR>_______________________________________________<BR>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org"> gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to <A 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">http://www.gromacs.org/mailing_lists/users.php</A><BR></BLOCKQUOTE> </DIV><BR><BR clear="all"><BR>-- <BR>Viswanadham Sridhara,<BR>Research Assistant,<BR>Old Dominion University,<BR>Norfolk, Va-23529.<DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>