[gmx-users] Re: NAN in g_anaeig -proj
Tsjerk Wassenaar
tsjerkw at gmail.com
Fri Oct 30 22:09:41 CET 2009
Hi Alex,
Unfortunately I don't have time to dig into that now. It might indeed
be a bug though and you might want to consider file a bugzilla report:
http://bugzilla.gromacs.org
That will put it on the table of the developers.
Cheers,
Tsjerk
2009/10/30 alexander yakovenko <yakovenko_a at ukr.net>:
> 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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--
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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