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
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</a><br>><br>><br>><br>><br>> --<br>> Viswanadham Sridhara,<br>> Research Assistant,<br>> Old Dominion University,<br>> Norfolk, Va-23529.<br>><br>>------------------------------------------------------------------------
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<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:\\www.biologie.uni-konstanz.de\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">
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</div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Research Assistant,<br>Old Dominion University,<br>Norfolk, Va-23529.