[gmx-users] PCA uses average structure or reference structure

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jun 25 22:15:46 CEST 2008

Hi Sunita,

You should check the manual on this (and some statistics texts on PCA).
g_covar calculates the average structure and takes the deviations
around this average for further calculations. In that respect, you
should be save. But the fact that you pose this question indicates
that you may be too little aware of what PCA is and can or can not do.

Hope it helps,


On Wed, Jun 25, 2008 at 3:59 PM, sunita gupta <sunita.bio at gmail.com> wrote:
> hi all
> I did MD studies of a dimer using NAMD and charmm forcefields.....now, in
> order analyze dynamic motions PCA was done using the command g_covar of
> GROMACS.....here i gave .trr and .pdb as input.....and selected backbone for
> analysis.....the output obtained were average.pdb, average.trr....etc....
> after that for analysing i used g_anaeig command.....providing average.trr
> as input.....to get filter.pdb....(after loading it in VMD i could see the
> global movement very clearly...)
> my query is that " in a paper i read that PCA analysis does not make any
> sense by using reference structure.....in fact average structure is the best
> choice".I am confused whether what i did was correct or not......
> and can anyone tell me how to use average structure in GROMACS
> --
> Member Research Team
> Lead Invent Technology
> TBIU, IIT Delhi, India
> Email- sunita at leadinvent.com
> Ph- +9111 26581524 (Ex-6)
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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