Mark, as I told previously to Justin ( lets to consider the problems with g_anaeig only in that topic to avoid producing doubles ) the problem is not in the average structure (it looks fine) but in the filter.xtc trajectory produced by g_anaeig. When I load that xtc to any structure in vmd I obtained dynamics picture of my protein with broken geometry (its look loke my protein was shrunken). But when I compared eigenvectors ( produced by g__covar) with the the results of the same cov.analysis where there were no such problems in filter.xtc I obtained full coverage in the same modes ( so g_covar in both cases produce apropriate cov.matrix and the problem only in g_anaeig .
James 2013/1/25 Mark Abraham <mark.j.abra...@gmail.com>: > On Tue, Jan 22, 2013 at 8:22 PM, James Starlight > <jmsstarli...@gmail.com>wrote: > >> Dear Gromacs users! >> >> >> There is some bug with g_anaeig the souce of which I could not fully >> understand. > > > Good Advice: until you can almost write a code patch to fix it, be very > hesitant in suggesting any software has a bug. The best people to help > solve the issue are often those who wrote the code, and you don't want them > annoyed with you :-) > > I have problems when I perform PCA of X-ray data set. >> Below you can my workflow. >> >> >> g_covar -f b2ar_xray_coors.pdb -s ref.pdb -o PCA_eigenval.xvg -v >> PCA_eigenvec.trr -av PCA_average.pdb -last 8 >> g_anaeig -v PCA_eigenvec.trr -s ref.pdb -f b2ar_xray_coors.pdb -rmsf >> eigrmsfPCA.xvg -filt >> >> >> here b2ar_xray_coors.pdb is the trajectory made from 10 X-ray >> structures of my protein (only main chain atoms are included) >> ref_pdb is the first frame of that trajectory >> >> >> As the result I've obtained reasonable eigenvalues and aigenvectors >> from g_covar BUT when I check filter trajectory ( produced by >> g_anaeig) fitted it to the ref.pdb or to the averaged structure in >> both cases I've obtained very distorted geometry of the protein in >> thefiltered trajectory. I have no such problems in case of PCA of MD >> trajectory ( when -f trajectory.trr is from the md snapshots not from >> x-ray structures) >> >> >> How it could be fixed ? >> > > How have you excluded the hypotheses that your reference structure is not a > valid representative of the middle of the range of variation? Or even that > the X-ray structural ensemble really is one? > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists