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 <tsje...@gmail.com>
Subject: Re: [gmx-users] NAN in g_anaeig -proj
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<8ff898150910300453n550a6358sf596cff4771c9...@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 <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)
>
>
>
>
>
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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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******************************************
Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
03143
acad.Zabolotnogo str. 150
Kiev
Ukraine
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E-mail: yakovenk...@ukr.net
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