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 <yakovenk...@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 <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) >> >> >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > 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 > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > 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: yakovenk...@ukr.net > > Не можешь найти работу? > 1,5 тысячи новых вакансий ежедневно на JOB.ukr.net. > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php