[gmx-users] dPCA analysis

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Feb 16 21:47:44 CET 2006

Hi Dongsheng,

IIRC, g_covar has an option -nofit That should do the trick.



On 2/16/06, Dongsheng Zhang <dong at pampas.chem.purdue.edu> wrote:
> Dear All,
> According to David's instruction at
> http://www.gromacs.org/pipermail/gmx-users/2005-October/017512.html
> gromax 3.3 can be used to do dPCA (dihedrals PCA) analysis by
> 1. g_angle -or to get angle.trr
> 2. g_covar -f angle.trr -s *.tpr to get eigenvec.trr
> 3. g_anaeig -f angle.trr -v eigenvec.trr -proj to get the projection of
> angle.trr on eigenvec.trr
> However, when I tried it in the way I mentioned above, I did not get
> what I expected. Therefore, I download Dr. Mu's code from
> http://www.gromacs.org/contributions/index.php
> and did the analysis again following Mu's recipe. I got a totally
> different result.
> After my investigation, I have a question regarding to the dPCA method
> in gromacs 3.3. In the conventional PCA, we need to remove the
> translational and rotational motion before generating the covariance
> matrix. That is what I think g_covar is actually doing.
> In dPCA, we should not do any modification of coordinates in angle.trr.
> I mean, no translation and rotation removal. This should be so because
> the dihedrals (or cos and sin) are internal coordinates.
> Then, I think we can not use g_covar directly to analyze angle.trr,
> rather we need to modify g_covar.
> Has anyone used the gmx3.3 to do dPCA analysis? If so please give me
> your comments on my thoughts. Thank you in advance!
> Best regards!
> Dongsheng
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060216/800ec087/attachment.html>

More information about the gromacs.org_gmx-users mailing list