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)
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