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.
