[gmx-users] Re: dPCA analysis

[Dongsheng Zhang]

Dear Daniela,


Thank you for your reply!


On Tue, 2006-02-21 at 16:30 +1000, Daniela S. Mueller wrote:
> dear dongsheng,
> 
> Dongsheng Zhang wrote:
> > Dear all,
> > 
> > Thank Tsjerk very much for the help. The option -nofit works for me.
> > However I still have some questions regarding g_covar:
> > 
> > 1. In g_covar analysis, it is required to have an input file for -s. It
> > can be *tpr or *pdb.  After I tested it, I found that the results
> > (eigenvalues and eigenvectors) were different by using *tpr or *pdb for
> > -s with the option -nofit. This is out of my expectation. With -nofit
> > option, I think *tpr serves as an index file to tell g_covar what
> > elements will be analyzed. I get the *tpr file by using:
> > tpbconv -s old.tpr -o *tpr -n index.ndx
> > by manipulating index.ndx, I can get different *tpr. Then I found I got
> > different results (eigenvalues and eigenvectors) with different *tpr
> > files in g_covar anlysis. I also changed coordinates in *pdb file, I got
> > the same results (That is the way it should be) with different *pdb
> > files. I think maybe something is wrong with the option -s *tpr. If
> > anyone knows the answer, please tell me. 
> 
> you are right that the tpr-file serves as a reference, but in order to 
> do that it has to match the atoms present in you trajectory. otherwise 
> you need an index-file for g_covar as well.
> usually the tpr-file should correspond to the set of atoms in the 
> trajectory- resp. structure-file that you are analysing.

I think tpr file has to match with trr file only respect to the number
of atomes, not the coordinates or atome names. In this sense, my tpr (7
atoms) matches with my angle.trr (21 coordinates), then I can't
understand why I can't get the right result. I try to add -n index.ndx.
It doesn't help.

Best wishes!

Dongsheng
> > 
> > 
> > Thank you for your help!
> > 
> > Dongsheng
> > 
> best regards,
> daniela
> 
> > 
> >>Message: 3
> >>Date: Thu, 16 Feb 2006 21:47:44 +0100
> >>From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> >>Subject: Re: [gmx-users] dPCA analysis
> >>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >>Message-ID:
> >>	<8ff898150602161247sf1ea3e6nbdba75d1f9e26447 at mail.gmail.com>
> >>Content-Type: text/plain; charset="iso-8859-1"
> >>
> >>Hi Dongsheng,
> >>
> >>IIRC, g_covar has an option -nofit That should do the trick.
> >>
> >>Cheers,
> >>
> >>Tsjerk
> >>
> >>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
> >>>
> >>
> >>--
> >>
> >>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
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