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
13588nan
13589nan
13590nan
(...)
13799nan
13800nan
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 InputFull 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
-inprinprod.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
-niceint19 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 int1 First eigenvector for analysis (-1 is select)
-lastint8 Last eigenvector for analysis (-1 is till the
last)
-skipint1 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 int2 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.
-tempreal 298.15 Temperature for entropy calculations
-nevskip int6 Number of eigenvalues to skip when computing the
entropy due to the quasi harmonic approximation.
When you
