<html>
<body>
<div style='font: 12pt sans-serif;'>
Hi Tsjerk!
<br />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.
<br />
<br />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:
<br />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
<br />so I can send you gzipped problem.
<br />Regards,
<br />Alex.
<br />
<br />
<blockquote class="ukr_editor_quotation" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">
<br />
<br />Message: 6
<br />Date: Fri, 30 Oct 2009 12:53:28 +0100
<br />From: Tsjerk Wassenaar <tsjerkw@gmail.com>
<br />Subject: Re: [gmx-users] NAN in g_anaeig -proj
<br />To: Discussion list for GROMACS users <gmx-users@gromacs.org>
<br />Message-ID:
<br /><8ff898150910300453n550a6358sf596cff4771c95b4@mail.gmail.com>
<br />Content-Type: text/plain; charset=ISO-8859-1
<br />
<br />Hi Alex,
<br />
<br />Sorry for not replying earlier. Still haven't had time to do checks
<br />myself. But have you already tried to see what happens if you only
<br />request projections?:
<br />
<br />g_anaeig_d -v sss_1000_eigenvec.trr -f sss_mdsi_1000.trr -s
<br />sss_mdsi_1000.tpr -first 1 -last 1 -n sss.ndx -proj
<br />
<br />Cheers,
<br />
<br />Tsjerk
<br />
<br />2009/10/29 alexander yakovenko <yakovenko_a@ukr.net>:
<br />> Hi all!
<br />> I just wonder if anyone run (know solution) into a problem trying to project
<br />> a trajectory on the eigenvector(s) (with g_anaeig -proj ) from covariace
<br />> matrix.
<br />> All projections I have calculated are nan. However, the eigenvalues are OK
<br />> and the g_anaeig -comp -v2 -eig2 -over options works OK so eigenvectors
<br />> seems are OK (but g_anaeig -2d fails to nan too). I am using gromacs-4.0.5
<br />> on x86-64 CentOS5 (compiled with gcc-34).
<br />> Regards,
<br />> Alex.
<br />> P.S. The sequence of commands that reveals the problem is attached bellow:
<br />>
<br />> g_covar_d -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -n sss.ndx -o
<br />> sss_1000_eigenval.xvg -xpm sss_1000_covar.xpm -v sss_1000_eigenvec.trr -mwa
<br />> -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
<br />> 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
<br />> 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
<br />> sss_1000_eigenvec.trr -eig2 sss_1000_eigenval.xvg -f sss_mdsi_1000.trr -s
<br />> 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
<br />> 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
<br />> sss_1000_eigenvec.trr
<br />> Read mass weighted average/minimum structure with 54 atoms from
<br />> 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
<br />> sss_1000_eigenvec.trr
<br />> Read mass weighted average/minimum structure with 54 atoms from
<br />> 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
<br />> ihm: Danke die bleibt wo sie ist" (Wir sind Helden)
<br />>
<br />>
<br />>
<br />>
<br />>
<br />> _______________________________________________
<br />> gmx-users mailing list gmx-users@gromacs.org
<br />> http://lists.gromacs.org/mailman/listinfo/gmx-users
<br />> Please search the archive at http://www.gromacs.org/search before posting!
<br />> Please don't post (un)subscribe requests to the list. Use the
<br />> www interface or send it to gmx-users-request@gromacs.org.
<br />> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
<br />>
<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 />
<br />------------------------------
<br />
<br />_______________________________________________
<br />gmx-users mailing list
<br />gmx-users@gromacs.org
<br />http://lists.gromacs.org/mailman/listinfo/gmx-users
<br />Please search the archive at http://www.gromacs.org/search before posting!
<br />
<br />End of gmx-users Digest, Vol 66, Issue 195
<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 />
<a href="http://www.ukr.net/2Bucwn/footer/804b93">Íå ìîæåøü íàéòè ðàáîòó?
<br />1,5 òûñÿ÷è íîâûõ âàêàíñèé åæåäíåâíî íà JOB.ukr.net</a>.
</div></body>
</html>