Hi Dongsheng,<br>
<br>
IIRC, g_covar has an option -nofit That should do the trick.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 2/16/06, <b class="gmail_sendername">Dongsheng Zhang</b> <<a href="mailto:dong@pampas.chem.purdue.edu">dong@pampas.chem.purdue.edu</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 All,<br><br>According to David's instruction at<br><a href="http://www.gromacs.org/pipermail/gmx-users/2005-October/017512.html">http://www.gromacs.org/pipermail/gmx-users/2005-October/017512.html</a><br><br>gromax 3.3
can be used to do dPCA (dihedrals PCA) analysis by<br>1. g_angle -or to get angle.trr<br>2. g_covar -f angle.trr -s *.tpr to get eigenvec.trr<br>3. g_anaeig -f angle.trr -v eigenvec.trr -proj to get the projection of<br>
angle.trr on eigenvec.trr<br><br>However, when I tried it in the way I mentioned above, I did not get<br>what I expected. Therefore, I download Dr. Mu's code from<br><a href="http://www.gromacs.org/contributions/index.php">
http://www.gromacs.org/contributions/index.php</a><br><br>and did the analysis again following Mu's recipe. I got a totally<br>different result.<br><br>After my investigation, I have a question regarding to the dPCA method
<br>in gromacs 3.3. In the conventional PCA, we need to remove the<br>translational and rotational motion before generating the covariance<br>matrix. That is what I think g_covar is actually doing.<br><br>In dPCA, we should not do any modification of coordinates in
angle.trr.<br>I mean, no translation and rotation removal. This should be so because<br>the dihedrals (or cos and sin) are internal coordinates.<br>Then, I think we can not use g_covar directly to analyze angle.trr,<br>rather we need to modify g_covar.
<br><br>Has anyone used the gmx3.3 to do dPCA analysis? If so please give me<br>your comments on my thoughts. Thank you in advance!<br><br>Best regards!<br><br>Dongsheng<br><br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>
Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>