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I'm using 4.0.2. There are three optional ndx flags, -n -sub -fr. As far as I can tell, -n defines the output group (will also set the fit group as the same), -sub tells you the frame numbers for cutting the trajectory into smaller sections and -fr also has something to do with frames. If you don't define an .ndx file then it will ask you for a fit group, but what I want is to specify a particular set of atoms (not CA, backbone, etc).<div><br></div><div>Maybe I'm just missing something simple. . . .</div><div><br></div><div>Josh<br><div><br></div><div><br></div><div><br></div><div><br><div><div>On Feb 26, 2009, at 11:12 AM, Berk Hess wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> Hi,<br><br>Which version of Gromacs are you using?<br>In 4.0, but I think also in 3.3, trjconv ask for both a fit and an output group.<br><br>Berk<br><br><hr id="stopSpelling">To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>From: <a href="mailto:jadelman@berkeley.edu">jadelman@berkeley.edu</a><br>Date: Thu, 26 Feb 2009 10:47:38 -0800<br>Subject: [gmx-users] trjconv fit subset of atoms<br><br> I am trying to use trjconv to generate a new .xtc file in which all frames have been aligned based on a subset of atoms (e.g. I have a multi-domain protein and I want to align the trajectory to one of the domains). Using a standard .ndx file only outputs the atoms associated with the fitted domain. I was wondering if there is a straightforward way to do what I describe without having to hack trjconv?<div><br></div><div>Looking at the source for do_fit.c it looks like if I were to set the mass of atoms that I didn't want to use in the alignment to zero, then it might work, but I am generally trying to avoid having to generate a tpr file since I'm coming from the pdb/psf world. </div><div><br></div><div>Any suggestions would be appreciated.</div><div><br></div><div>Josh<br><br><div> <span class="EC_Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style="margin-right: 0px; margin-bottom: 0px; margin-left: 0px;">------------------------------------------------------------------------------------------------------</div><div style="margin-right: 0px; margin-bottom: 0px; margin-left: 0px;">Joshua L. Adelman</div><div style="margin-right: 0px; margin-bottom: 0px; margin-left: 0px;">Biophysics Graduate Group Lab: 510.643.2159</div><div style="margin-right: 0px; margin-bottom: 0px; margin-left: 0px;">218 Wellman Hall Fax: 510.642.7428</div><div style="margin-right: 0px; margin-bottom: 0px; margin-left: 0px;">University of California, Berkeley <a href="http://nature.berkeley.edu/%7Ejadelman">http://nature.berkeley.edu/~jadelman</a></div><div style="margin-right: 0px; margin-bottom: 0px; margin-left: 0px;">Berkeley, CA 94720 USA <a href="mailto:jadelman@berkeley.edu">jadelman@berkeley.edu</a></div><div style="margin-right: 0px; margin-bottom: 0px; margin-left: 0px;">------------------------------------------------------------------------------------------------------</div><br class="EC_Apple-interchange-newline"></span> </div><br></div><br><hr>See all the ways you can stay connected <a href="http://www.microsoft.com/windows/windowslive/default.aspx" target="_new">to friends and family</a><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 search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!</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. 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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> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><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; ">Joshua L. Adelman</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Biophysics Graduate Group Lab: 510.643.2159</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">218 Wellman Hall Fax: 510.642.7428</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">University of California, Berkeley <a href="http://nature.berkeley.edu/~jadelman">http://nature.berkeley.edu/~jadelman</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Berkeley, CA 94720 USA <a href="mailto:jadelman@berkeley.edu">jadelman@berkeley.edu</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------------------------------------</div><br class="Apple-interchange-newline"></span> </div><br></div></div></body></html>