[gmx-users] nan in g_anaeig -over
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Jul 26 17:48:02 CEST 2012
On 27/07/2012 12:31 AM, Joaquim Rui de Castro Rodrigues wrote:
> 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)--
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Something's wrong with your eigenvectors. Look at the other output files
and/or gmxdump the eigenvector files.
Mark
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