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, Tsjerk On Wed, Jun 25, 2008 at 3:59 PM, sunita gupta <[EMAIL PROTECTED]> 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 > > > -- > SUNITA GUPTA > Member Research Team > Lead Invent Technology > TBIU, IIT Delhi, India > Email- [EMAIL PROTECTED] > Ph- +9111 26581524 (Ex-6) > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php