Hi Alex, Sorry for not replying earlier. Still haven't had time to do checks myself. But have you already tried to see what happens if you only request projections?:
g_anaeig_d -v sss_1000_eigenvec.trr -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -first 1 -last 1 -n sss.ndx -proj Cheers, Tsjerk 2009/10/29 alexander yakovenko <yakovenk...@ukr.net>: > Hi all! > I just wonder if anyone run (know solution) into a problem trying to project > a trajectory on the eigenvector(s) (with g_anaeig -proj ) from covariace > matrix. > All projections I have calculated are nan. However, the eigenvalues are OK > and the g_anaeig -comp -v2 -eig2 -over options works OK so eigenvectors > seems are OK (but g_anaeig -2d fails to nan too). I am using gromacs-4.0.5 > on x86-64 CentOS5 (compiled with gcc-34). > Regards, > Alex. > P.S. The sequence of commands that reveals the problem is attached bellow: > > g_covar_d -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -n sss.ndx -o > sss_1000_eigenval.xvg -xpm sss_1000_covar.xpm -v sss_1000_eigenvec.trr -mwa > -l > ... > Option Filename Type Description > ------------------------------------------------------------ > -f sss_mdsi_1000.trr Input Trajectory: xtc trr trj gro g96 pdb cpt > -s sss_mdsi_1000.tpr Input Structure+mass(db): tpr tpb tpa gro g96 > pdb > -n sss.ndx Input, Opt! Index file > -o sss_1000_eigenval.xvg Output xvgr/xmgr file > -v sss_1000_eigenvec.trr Output Full precision trajectory: trr trj > cpt > -av average.pdb Output Structure file: gro g96 pdb > -l covar.log Output Log file > -ascii covar.dat Output, Opt. Generic data file > -xpm sss_1000_covar.xpm Output, Opt! X PixMap compatible matrix file > -xpma covara.xpm Output, Opt. X PixMap compatible matrix file > > Option Type Value Description > ------------------------------------------------------ > -[no]h bool no Print help info and quit > -nice int 19 Set the nicelevel > -b time 0 First frame (ps) to read from trajectory > -e time 0 Last frame (ps) to read from trajectory > -dt time 0 Only use frame when t MOD dt = first time (ps) > -tu enum ps Time unit: ps, fs, ns, us, ms or s > -[no]xvgr bool yes Add specific codes (legends etc.) in the output > xvg files for the xmgrace program > -[no]fit bool yes Fit to a reference structure > -[no]ref bool no Use the deviation from the conformation in the > structure file instead of from the average > -[no]mwa bool yes Mass-weighted covariance analysis > -last int -1 Last eigenvector to write away (-1 is till the > last) > -[no]pbc bool yes Apply corrections for periodic boundary > conditions > > Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision) > Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision) > > Choose a group for the least squares fit > Group 0 ( System) has 31748 elements > ... > Group 20 ( active_site) has 54 elements > Select a group: 20 > Selected 20: 'active_site' > > Choose a group for the covariance analysis > Group 0 ( System) has 31748 elements > ... > Group 20 ( active_site) has 54 elements > Select a group: 20 > Selected 20: 'active_site' > Calculating the average structure ... > trn version: GMX_trn_file (double precision) > Last frame 2000 time 2000.000 > > Constructing covariance matrix (162x162) ... > Last frame 2000 time 2000.000 > Read 2001 frames > > Trace of the covariance matrix: 6.22756 (u nm^2) > > 100% > Diagonalizing ... > > Sum of the eigenvalues: 6.22756 (u nm^2) > > Writing eigenvalues to sss_1000_eigenval.xvg > > Writing reference, average structure & eigenvectors 1--162 to > sss_1000_eigenvec.trr > > Wrote the log to covar.log > > gcq#86: "Shake Barrels Of Whisky Down My Throat" (Throwing Muses) > > > > g_anaeig_d -v sss_1000_eigenvec.trr -eig sss_1000_eigenval.xvg -v2 > sss_1000_eigenvec.trr -eig2 sss_1000_eigenval.xvg -f sss_mdsi_1000.trr -s > sss_mdsi_1000.tpr -first 1 -last 10 -n sss.ndx -proj -over > > ... > > Option Filename Type Description > ------------------------------------------------------------ > -v sss_1000_eigenvec.trr Input Full precision trajectory: trr trj > cpt > -v2 sss_1000_eigenvec.trr Input, Opt! Full precision trajectory: trr trj > cpt > -f sss_mdsi_1000.trr Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt > -s sss_mdsi_1000.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 > pdb > -n sss.ndx Input, Opt! Index file > -eig sss_1000_eigenval.xvg Input, Opt! xvgr/xmgr file > -eig2sss_1000_eigenval.xvg Input, Opt! xvgr/xmgr file > -comp eigcomp.xvg Output, Opt. xvgr/xmgr file > -rmsf eigrmsf.xvg Output, Opt. xvgr/xmgr file > -proj proj.xvg Output, Opt! xvgr/xmgr file > -2d 2dproj.xvg Output, Opt. xvgr/xmgr file > -3d 3dproj.pdb Output, Opt. Structure file: gro g96 pdb > -filt filtered.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt > -extr extreme.pdb Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt > -over overlap.xvg Output, Opt! xvgr/xmgr file > -inpr inprod.xpm Output, Opt. X PixMap compatible matrix file > > Option Type Value Description > ------------------------------------------------------ > -[no]h bool no Print help info and quit > -nice int 19 Set the nicelevel > -b time 0 First frame (ps) to read from trajectory > -e time 0 Last frame (ps) to read from trajectory > -dt time 0 Only use frame when t MOD dt = first time (ps) > -tu enum ps Time unit: ps, fs, ns, us, ms or s > -[no]w bool no View output xvg, xpm, eps and pdb files > -[no]xvgr bool yes Add specific codes (legends etc.) in the output > xvg files for the xmgrace program > -first int 1 First eigenvector for analysis (-1 is select) > -last int 10 Last eigenvector for analysis (-1 is till the > last) > -skip int 1 Only analyse every nr-th frame > -max real 0 Maximum for projection of the eigenvector on the > average structure, max=0 gives the extremes > -nframes int 2 Number of frames for the extremes output > -[no]split bool no Split eigenvector projections where time is zero > -[no]entropy bool no Compute entropy according to the Quasiharmonic > formula or Schlitter's method. > -temp real 298.15 Temperature for entropy calculations > -nevskip int 6 Number of eigenvalues to skip when computing the > entropy due to the quasi harmonic approximation. > When you do a rotational and/or translational > fit > prior to the covariance analysis, you get 3 or 6 > eigenvalues that are very close to zero, and > which should not be taken into account when > computing the entropy. > > trn version: GMX_trn_file (double precision) > Read mass weighted reference structure with 54 atoms from > sss_1000_eigenvec.trr > Read mass weighted average/minimum structure with 54 atoms from > sss_1000_eigenvec.trr > Read 162 eigenvectors (for 54 atoms) > > Read 162 eigenvalues from sss_1000_eigenval.xvg > Read mass weighted reference structure with 54 atoms from > sss_1000_eigenvec.trr > Read mass weighted average/minimum structure with 54 atoms from > sss_1000_eigenvec.trr > Read 162 eigenvectors (for 54 atoms) > > Read 162 eigenvalues from sss_1000_eigenval.xvg > Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision) > Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision) > > Note: the structure in sss_mdsi_1000.tpr should be the same > as the one used for the fit in g_covar > > Select the index group that was used for the least squares fit in g_covar > Group 0 ( System) has 31748 elements > ... > Group 20 ( active_site) has 54 elements > Select a group: 20 > Selected 20: 'active_site' > > Select an index group of 54 elements that corresponds to the eigenvectors > Group 0 ( System) has 31748 elements > ... > Group 20 ( active_site) has 54 elements > Select a group: 20 > Selected 20: 'active_site' > > RMSD (without fit) between the two average structures: 0.000 (nm) > > 10 eigenvectors selected for output: 1 2 3 4 5 6 7 8 9 10 > Last frame 2000 time 2000.000 > > Calculating overlap between eigenvectors of set 2 with eigenvectors > 1 2 3 4 5 6 7 8 9 10 > > Will compare the covariance matrices using 162 dimensions > Trace of the two matrices: 6.22756 and 6.22756 > Square root of the traces: 2.49551 and 2.49551 > The overlap of the covariance matrices: > normalized: 1.000 > shape: 1.000 > > gcq#334: "Aber wenn der Quarterback kommt, um dir die Brille abzunehmen Sag > ihm: Danke die bleibt wo sie ist" (Wir sind Helden) > > > > > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
