[gmx-users] nan in g_anaeig -over

[Joaquim Rui de Castro Rodrigues]

Dear all,
 
I am getting a nan while calculating the overlap between covariance matrices (in this case, using the same vectors for -v and -v2): 
g_anaeig455 -v atp/eigenvectors.trr -v2 atp/eigenvectors.trr -over overlap_atp-atp
 
I tried different gromacs versions, different -last values, and also setting the -eig and -eig2 flags, with the same results.
Any idea what could be wrong here?
Please find below the content of the .xvg file and the ouput from g_anaeig.
 
Thanks for your time,
Rui Rodrigues
 
 
 
Here is the content of overlap_atp-atp.xvg:
@    title "Subspace overlap"
@    xaxis  label "Eigenvectors of trajectory 2"
@    yaxis  label "Overlap"
@TYPE xy
@ subtitle "using 8 eigenvectors of trajectory 1"
    1  0.125
    2  0.250
    3  0.375
    4  0.500
    5  0.625
    6  0.750
    7  0.875
    8  1.000
    9  1.000
   10  1.000
(...)
13586  1.000
13587  1.000
13588    nan
13589    nan
13590    nan
(...)
13799    nan
13800    nan

 
Here is the complete ouput from g_anaeig:
                         :-)  G  R  O  M  A  C  S  (-:
                              S  C  A  M  O  R  G
                            :-)  VERSION 4.5.5  (-:
        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
      Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
        Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
                Michael Shirts, Alfons Sijbers, Peter Tieleman,
               Berk Hess, David van der Spoel, and Erik Lindahl.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2010, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            check out http://www.gromacs.org for more information.
         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.
                :-)  /usr/local/gromacs455/bin/g_anaeig455  (-:
Option     Filename  Type         Description
------------------------------------------------------------
  -v atp/eigenvectors.trr  Input        Full precision trajectory: trr trj cpt
 -v2 atp/eigenvectors.trr  Input, Opt!  Full precision trajectory: trr trj cpt
  -f       traj.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
  -s      topol.tpr  Input, Opt.  Structure+mass(db): tpr tpb tpa gro g96 pdb
  -n      index.ndx  Input, Opt.  Index file
-eig   eigenval.xvg  Input, Opt.  xvgr/xmgr file
-eig2 eigenval2.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 etc.
-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
-overoverlap_atp-atp.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
-[no]version bool   no      Print version 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: fs, ps, ns, us, ms or s
-[no]w       bool   no      View output .xvg, .xpm, .eps and .pdb files
-xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-first       int    1       First eigenvector for analysis (-1 is select)
-last        int    8       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 (single precision)
Read non mass weighted reference structure with 4600 atoms from atp/eigenvectors.trr
Read non mass weighted average/minimum structure with 4600 atoms from atp/eigenvectors.trr
Read 13800 eigenvectors (for 4600 atoms)
Read non mass weighted reference structure with 4600 atoms from atp/eigenvectors.trr
Read non mass weighted average/minimum structure with 4600 atoms from atp/eigenvectors.trr
Read 13800 eigenvectors (for 4600 atoms)
8 eigenvectors selected for output: 1 2 3 4 5 6 7 8
Calculating overlap between eigenvectors of set 2 with eigenvectors
1 2 3 4 5 6 7 8
RMSD (without fit) between the two average structures: 0.000 (nm)
Will compare the covariance matrices using 13800 dimensions
Trace of the two matrices: 339.752 and 339.752
Square root of the traces: 18.4324 and 18.4324
The overlap of the covariance matrices:
  normalized:  nan
       shape:  nan
gcq#97: "The Universe is Somewhere In Here" (J.G.E.M. Fraaije)