Hi Bin, Did you use the same force field, simulation length, other parameters? The system size might play a role too. And for trialanine the reference used for fitting may matter too. But first check all the other similarities/differences.
Cheers, Tsjerk On Jan 8, 2016 16:35, "Bin Liu" <fdusuperstr...@gmail.com> wrote: > Hi Tsjerk, > > I used trjconv -pbc and trjconv -nojump to remove PBC and jump across the > boundary before I applied g_covar. This paper is about dPCA indeed. But it > also contains the author's results on cPCA. Thank you for your help. > > Regards, > > Bin > > > > Message: 6 > Date: Thu, 7 Jan 2016 23:38:44 +0100 > From: Tsjerk Wassenaar <tsje...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] Correct method to do Cartesian PCA > Message-ID: > < > cabze1shyqdeg4sexss5qtjcy7qfg8s+2jsh3pmchufh4xnr...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Bin, > > The procedure is correct, provided you ensured that the input trajectory > did not have PBC jumps. But the paper you refer to is on dihedral angle > PCA... > > Cheers, > > Tsjerk > On Jan 7, 2016 23:06, "Bin Liu" <fdusuperstr...@gmail.com> wrote: > > > Hi All, > > > > I am trying to reproduce the Cartesian PCA results for ALA3 in water by > > Altis et al. (Fig.2 of Dihedral angle principal component analysis of > > molecular dynamics simulations. http://dx.doi.org/10.1063/1.2746330 ) > > It is probably the most well-known PCA analysis results. I created a > system > > as they suggested and got a 100 ns trajectory (after an equilibration > > stage) for applying PCA. > > > > GROMOS96 43a1 > > SPC water > > 300 K, 1 atm > > PME > > cutoff 1.0 nm > > Box larger than they did, 2100~ waters > > > > As all the PCA tutorials indicate, applying Cartesian PCA can be as > simple > > as two commands, g_covar and g_anaeig. However with all my effort of > trying > > all the combinations of arguments I can think of, I still can't reproduce > > the literature results. Here I humbly request help from experienced users > > who have applied PCA before. > > > > The following is my approach. Suppose I have a .tpr file > *npt_pr_100ns.tpr* > > and a .trr file *npt_pr_100ns.trr* > > > > *g_covar -s npt_pr_100ns.tpr -f npt_pr_100ns.trr -o eigenval.xvg -v > > eigenvec.trr -av average.pdb -l covar.log* > > Choose a group for the least squares fit > > Group 0 ( System) has 6518 elements > > Group 1 ( Protein) has 22 elements > > Group 2 ( Protein-H) has 16 elements > > ... > > Select a group: 1 > > Selected 1: 'Protein' > > > > Choose a group for the covariance analysis > > Group 0 ( System) has 6518 elements > > Group 1 ( Protein) has 22 elements > > Group 2 ( Protein-H) has 16 elements > > ... > > Select a group: 1 > > Selected 1: 'Protein' > > > > *g_anaeig -v eigenvec.trr > > -f npt_pr_100ns.trr -s npt_pr_100ns.tpr -2d 2dproj.xvg -first 1 -last 2* > > > > Select the index group that was used for the least squares fit in g_covar > > Group 0 ( System) has 6518 elements > > Group 1 ( Protein) has 22 elements > > Group 2 ( Protein-H) has 16 elements > > ... > > Select a group: 1 > > Selected 1: 'Protein' > > > > Select an index group of 22 elements that corresponds to the eigenvectors > > Group 0 ( System) has 6518 elements > > Group 1 ( Protein) has 22 elements > > Group 2 ( Protein-H) has 16 elements > > ... > > Select a group: 1 > > Selected 1: 'Protein' > > > > Is there anything I did incorrectly? Another question: is -mwa argument > > which turns on mass weighting for g_covar necessary? Thank you very > much. > > > > Best Regards, > > > > Bin > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
