[gmx-users] Re: NAN in g_anaeig -proj

alexander yakovenko yakovenko_a at ukr.net
Fri Oct 30 16:59:40 CET 2009


Hi Tsjerk!  
That is where I encountered NANs problem (except it was 10 eigenvectos, but for 1 NANs appears as well). I used -over option to check eigenvectors only.  
  
Now it seems for me that it is a bug and not my stupid typing mistake. What can really help in this case (IMHO!) is my problem in your debugger - I found that the problem appears even if I try to project trajectory of single frame gro file:  
g_anaeig_d -v sss_1000_eigenvec.trr -f sss_after_mdsi_1000.gro -s sss_mdsi_1000.tpr -first 1 -last 1 -n sss.ndx -proj  
so I can send you gzipped problem.  
Regards,  
Alex.  
  
    
  
Message: 6  
Date: Fri, 30 Oct 2009 12:53:28 +0100  
From: Tsjerk Wassenaar <tsjerkw at gmail.com>  
Subject: Re: [gmx-users] NAN in g_anaeig -proj  
To: Discussion list for GROMACS users <gmx-users at gromacs.org>  
Message-ID:  
<8ff898150910300453n550a6358sf596cff4771c95b4 at mail.gmail.com>  
Content-Type: text/plain; charset=ISO-8859-1  
  
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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End of gmx-users Digest, Vol 66, Issue 195  
******************************************  
  
  
  
Alexander Yakovenko  
Institute of Molecular Biology & Genetic of NAS of Ukraine  
03143  
acad.Zabolotnogo str. 150  
Kiev  
Ukraine  
______________________________________________  
E-mail: yakovenko_a at ukr.net  
  
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