[gmx-users] Re: dPCA analysis
dong at pampas.chem.purdue.edu
Tue Feb 21 06:45:23 CET 2006
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.
2. The eigenvalues have been used as time (after t=-1, 0) in the ouput
file eigenvec.trr from g_covar (in gmx3.3) analysis. This causes
segmentation fault in the further analysis g_anaeig. Has anyone used
g_covar and g_anaeig in gmx3.3? Why did I get such a strange behavior?
(By the way, g_covar and g_anaeig in gmx 3.2 work fine)
Thank you for your help!
> 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>
> <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.
> 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
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> 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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