[gmx-users] nan in g_anaeig -over
Joaquim Rui de Castro Rodrigues
joaquim.rodrigues at ipleiria.pt
Thu Jul 26 16:31:57 CEST 2012
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, PÃ¤r 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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