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<div>Thank you, Tsjerk, for replay.
<br />my commands:
<br />
<br />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
<br />...
<br />Option Filename Type Description
<br />------------------------------------------------------------
<br /> -f sss_mdsi_1000.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
<br /> -s sss_mdsi_1000.tpr Input Structure+mass(db): tpr tpb tpa gro g96
<br /> pdb
<br /> -n sss.ndx Input, Opt! Index file
<br /> -o sss_1000_eigenval.xvg Output xvgr/xmgr file
<br /> -v sss_1000_eigenvec.trr Output Full precision trajectory: trr trj
<br /> cpt
<br /> -av average.pdb Output Structure file: gro g96 pdb
<br /> -l covar.log Output Log file
<br />-ascii covar.dat Output, Opt. Generic data file
<br />-xpm sss_1000_covar.xpm Output, Opt! X PixMap compatible matrix file
<br />-xpma covara.xpm Output, Opt. X PixMap compatible matrix file
<br />
<br />Option Type Value Description
<br />------------------------------------------------------
<br />-[no]h bool no Print help info and quit
<br />-nice int 19 Set the nicelevel
<br />-b time 0 First frame (ps) to read from trajectory
<br />-e time 0 Last frame (ps) to read from trajectory
<br />-dt time 0 Only use frame when t MOD dt = first time (ps)
<br />-tu enum ps Time unit: ps, fs, ns, us, ms or s
<br />-[no]xvgr bool yes Add specific codes (legends etc.) in the output
<br /> xvg files for the xmgrace program
<br />-[no]fit bool yes Fit to a reference structure
<br />-[no]ref bool no Use the deviation from the conformation in the
<br /> structure file instead of from the average
<br />-[no]mwa bool yes Mass-weighted covariance analysis
<br />-last int -1 Last eigenvector to write away (-1 is till the
<br /> last)
<br />-[no]pbc bool yes Apply corrections for periodic boundary conditions
<br />
<br />Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
<br />Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
<br />
<br />Choose a group for the least squares fit
<br />Group 0 ( System) has 31748 elements
<br />...
<br />Group 20 ( active_site) has 54 elements
<br />Select a group: 20
<br />Selected 20: 'active_site'
<br />
<br />Choose a group for the covariance analysis
<br />Group 0 ( System) has 31748 elements
<br />...
<br />Group 20 ( active_site) has 54 elements
<br />Select a group: 20
<br />Selected 20: 'active_site'
<br />Calculating the average structure ...
<br />trn version: GMX_trn_file (double precision)
<br />Last frame 2000 time 2000.000
<br />
<br />Constructing covariance matrix (162x162) ...
<br />Last frame 2000 time 2000.000
<br />Read 2001 frames
<br />
<br />Trace of the covariance matrix: 6.22756 (u nm^2)
<br />
<br />100%
<br />Diagonalizing ...
<br />
<br />Sum of the eigenvalues: 6.22756 (u nm^2)
<br />
<br />Writing eigenvalues to sss_1000_eigenval.xvg
<br />
<br />Writing reference, average structure & eigenvectors 1--162 to sss_1000_eigenvec.trr
<br />
<br />Wrote the log to covar.log
<br />
<br />gcq#86: "Shake Barrels Of Whisky Down My Throat" (Throwing Muses)
<br />
<br />
<br />
<br />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
<br />
<br />...
<br />
<br />Option Filename Type Description
<br />------------------------------------------------------------
<br /> -v sss_1000_eigenvec.trr Input Full precision trajectory: trr trj
<br /> cpt
<br /> -v2 sss_1000_eigenvec.trr Input, Opt! Full precision trajectory: trr trj
<br /> cpt
<br /> -f sss_mdsi_1000.trr Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt
<br /> -s sss_mdsi_1000.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96
<br /> pdb
<br /> -n sss.ndx Input, Opt! Index file
<br />-eig sss_1000_eigenval.xvg Input, Opt! xvgr/xmgr file
<br />-eig2sss_1000_eigenval.xvg Input, Opt! xvgr/xmgr file
<br />-comp eigcomp.xvg Output, Opt. xvgr/xmgr file
<br />-rmsf eigrmsf.xvg Output, Opt. xvgr/xmgr file
<br />-proj proj.xvg Output, Opt! xvgr/xmgr file
<br /> -2d 2dproj.xvg Output, Opt. xvgr/xmgr file
<br /> -3d 3dproj.pdb Output, Opt. Structure file: gro g96 pdb
<br />-filt filtered.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
<br />-extr extreme.pdb Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
<br />-over overlap.xvg Output, Opt! xvgr/xmgr file
<br />-inpr inprod.xpm Output, Opt. X PixMap compatible matrix file
<br />
<br />Option Type Value Description
<br />------------------------------------------------------
<br />-[no]h bool no Print help info and quit
<br />-nice int 19 Set the nicelevel
<br />-b time 0 First frame (ps) to read from trajectory
<br />-e time 0 Last frame (ps) to read from trajectory
<br />-dt time 0 Only use frame when t MOD dt = first time (ps)
<br />-tu enum ps Time unit: ps, fs, ns, us, ms or s
<br />-[no]w bool no View output xvg, xpm, eps and pdb files
<br />-[no]xvgr bool yes Add specific codes (legends etc.) in the output
<br /> xvg files for the xmgrace program
<br />-first int 1 First eigenvector for analysis (-1 is select)
<br />-last int 10 Last eigenvector for analysis (-1 is till the
<br /> last)
<br />-skip int 1 Only analyse every nr-th frame
<br />-max real 0 Maximum for projection of the eigenvector on the
<br /> average structure, max=0 gives the extremes
<br />-nframes int 2 Number of frames for the extremes output
<br />-[no]split bool no Split eigenvector projections where time is zero
<br />-[no]entropy bool no Compute entropy according to the Quasiharmonic
<br /> formula or Schlitter's method.
<br />-temp real 298.15 Temperature for entropy calculations
<br />-nevskip int 6 Number of eigenvalues to skip when computing the
<br /> entropy due to the quasi harmonic approximation.
<br /> When you do a rotational and/or translational fit
<br /> prior to the covariance analysis, you get 3 or 6
<br /> eigenvalues that are very close to zero, and
<br /> which should not be taken into account when
<br /> computing the entropy.
<br />
<br />trn version: GMX_trn_file (double precision)
<br />Read mass weighted reference structure with 54 atoms from sss_1000_eigenvec.trr
<br />Read mass weighted average/minimum structure with 54 atoms from sss_1000_eigenvec.trr
<br />Read 162 eigenvectors (for 54 atoms)
<br />
<br />Read 162 eigenvalues from sss_1000_eigenval.xvg
<br />Read mass weighted reference structure with 54 atoms from sss_1000_eigenvec.trr
<br />Read mass weighted average/minimum structure with 54 atoms from sss_1000_eigenvec.trr
<br />Read 162 eigenvectors (for 54 atoms)
<br />
<br />Read 162 eigenvalues from sss_1000_eigenval.xvg
<br />Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
<br />Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)
<br />
<br />Note: the structure in sss_mdsi_1000.tpr should be the same
<br /> as the one used for the fit in g_covar
<br />
<br />Select the index group that was used for the least squares fit in g_covar
<br />Group 0 ( System) has 31748 elements
<br />...
<br />Group 20 ( active_site) has 54 elements
<br />Select a group: 20
<br />Selected 20: 'active_site'
<br />
<br />Select an index group of 54 elements that corresponds to the eigenvectors
<br />Group 0 ( System) has 31748 elements
<br />...
<br />Group 20 ( active_site) has 54 elements
<br />Select a group: 20
<br />Selected 20: 'active_site'
<br />
<br />RMSD (without fit) between the two average structures: 0.000 (nm)
<br />
<br />10 eigenvectors selected for output: 1 2 3 4 5 6 7 8 9 10
<br />Last frame 2000 time 2000.000
<br />
<br />Calculating overlap between eigenvectors of set 2 with eigenvectors
<br />1 2 3 4 5 6 7 8 9 10
<br />
<br />Will compare the covariance matrices using 162 dimensions
<br />Trace of the two matrices: 6.22756 and 6.22756
<br />Square root of the traces: 2.49551 and 2.49551
<br />The overlap of the covariance matrices:
<br /> normalized: 1.000
<br /> shape: 1.000
<br />
<br />gcq#334: "Aber wenn der Quarterback kommt, um dir die Brille abzunehmen Sag ihm: Danke die bleibt wo sie ist" (Wir sind Helden)
<br />
<br />
<br />
<br /></div>
<br />
<blockquote class="ukr_editor_quotation" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">From: Tsjerk Wassenaar <tsjerkw@gmail.com>
<br />Subject: Re: [gmx-users] nans in g_anaeig
<br />To: Discussion list for GROMACS users <gmx-users@gromacs.org>
<br />Message-ID:
<br /><8ff898150910271319n5a10949aq13298eebb119c635@mail.gmail.com>
<br />Content-Type: text/plain; charset=ISO-8859-1
<br />
<br />Hi Alex,
<br />
<br />Can you paste the actual sequence of commands you used?
<br />
<br />Cheers,
<br />
<br />Tsjerk
<br />
<br />2009/10/27 alexander yakovenko <yakovenko_a@ukr.net>:
<br />> Hi all!
<br />> I run into a problem trying to project trajectory on the eigenvector(s)
<br />> (with g_anaeig -proj ) from covariace matrix - all projections are nan. The
<br />> eigenvalues are OK, the g_anaeig -comp -v2 -eig2 -over options works OK so
<br />> eigenvectors seems are OK (but g_anaeig -2d fails to nan too). I am using
<br />> gromacs-4.0.5 on x86-64 CentOS5 (compiled with gcc-34).
<br />> What can help me to project it properly?
<br />> Regards,
<br />> Alex.
<br />>
<br />>
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<br />
<br />--
<br />Tsjerk A. Wassenaar, Ph.D.
<br />Junior UD (post-doc)
<br />Biomolecular NMR, Bijvoet Center
<br />Utrecht University
<br />Padualaan 8
<br />3584 CH Utrecht
<br />The Netherlands
<br />P: +31-30-2539931
<br />F: +31-30-2537623
<br />
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<br />End of gmx-users Digest, Vol 66, Issue 174
<br />******************************************
<br />
<br /></blockquote>
<br />
<br />Alexander Yakovenko
<br />Institute of Molecular Biology & Genetic of NAS of Ukraine
<br />03143
<br />acad.Zabolotnogo str. 150
<br />Kiev
<br />Ukraine
<br />______________________________________________
<br />E-mail: yakovenko_a@ukr.net
<br />
<br />
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