[gmx-users] NAN in g_anaeig -proj
Tsjerk Wassenaar
tsjerkw at gmail.com
Fri Oct 30 12:53:28 CET 2009
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 <yakovenko_a at 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)
>
>
>
>
>
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--
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
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