[gmx-users] Re: dPCA analysis

Daniela S. Mueller d.s.mueller at rug.nl
Tue Feb 21 07:30:21 CET 2006

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.
> Thank you for your help!
> Dongsheng
best regards,

>>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
>>>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
>>>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!
>>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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Daniela S. Mueller

Diplom biologist

-Molecular Dynamics Group, UQ -

School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane

Phone: +61-7-33653732
Email: d.s.mueller at uq.edu.au

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm


- MD group, RuG -

Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Email: d.s.mueller at rug.nl

Website: http://www.rug.nl/gbb/md

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