Dear all, We are performing some PCA analysis of several 22ns trajectories of a protein hexamer at different temperatures (280, 300, 320K). We expected to see a similar movement decribed by the ~10 lowest PCA's. their overlap is very poor: Below 0.35, and the diagonal elements are not remarkably higher than the rest. If we split one of the trajectories into to 11ns ones and do the same, again the overlap obtained is below 0.44 in all cases and there is no clear diagonal. 11ns is quite a long trajectory so I expected to see the same type of movement described by both 11ns fragments. Here are the cosine contents of the whole 22 ns trajectory and the two fragments. Except for the 1st pc, the rest seem well sampled: shouldn't they agree? 22ns: Cosine content PC1 0.956255 Cosine content PC2 0.00428106 Cosine content PC3 0.000162083
1st 11ns: Cosine content PC1 0.923261 Cosine content PC2 0.0217681 Cosine content PC3 0.0135543 2nd 11ns: Cosine content PC1 0.786694 Cosine content PC2 0.1654 Cosine content PC3 0.000335589 Are we doing something wrong? Is this the exptected behaviour? This is what we do to calculate the PCA's (10ns of equilibration removed): g_covar -f trajectory.xtc -b 10000 -e 21000 -s structure.pdb -o eigenval-T300-A.xvg -v eigenvec-T300-A.trr -av average-pca-T300-A.pdb g_covar -f trajectory.xtc -b 21020 -s structure.pdb -o eigenval-T300-B.xvg -v eigenvec-T300-B.trr -av average-pca-T300-B.pdb and to compare them: g_anaeig -inpr T300-A-B.xpm -v eigenvec-T300-A.trr -v2 eigenvec-T300-B.trr -first 1 -last 10 Thanks for your help and suggestions! Ramon _______________________________________________ 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