NAME

       g_covar - calculates and diagonalizes the covariance matrix

       VERSION 4.6.5

SYNOPSIS

       g_covar  -f  traj.xtc  -s  topol.tpr  -n  index.ndx  -o  eigenval.xvg  -v eigenvec.trr -av
       average.pdb  -l  covar.log  -ascii  covar.dat  -xpm  covar.xpm  -xpma  covara.xpm   -[no]h
       -[no]version  -nice  int  -b  time  -e  time -dt time -tu enum -xvg enum -[no]fit -[no]ref
       -[no]mwa -last int -[no]pbc

DESCRIPTION

         g_covar  calculates  and  diagonalizes  the  (mass-weighted)  covariance  matrix.    All
       structures  are  fitted  to  the  structure in the structure file.  When this is not a run
       input file periodicity will not be taken into account. When the fit  and  analysis  groups
       are  identical  and  the  analysis  is  non  mass-weighted,  the  fit  will  also  be  non
       mass-weighted.

       The eigenvectors are written to a trajectory file ( -v).  When the same atoms are used for
       the  fit and the covariance analysis, the reference structure for the fit is written first
       with t=-1.  The average (or reference when  -ref is used) structure is written  with  t=0,
       the eigenvectors are written as frames with the eigenvector number as timestamp.

       The eigenvectors can be analyzed with  g_anaeig.

       Option   -ascii  writes  the  whole  covariance  matrix to an ASCII file. The order of the
       elements is: x1x1, x1y1, x1z1, x1x2, ...

       Option  -xpm writes the whole covariance matrix to an  .xpm file.

       Option  -xpma writes the atomic covariance matrix to an  .xpm file,  i.e.  for  each  atom
       pair the sum of the xx, yy and zz covariances is written.

       Note  that  the diagonalization of a matrix requires memory and time that will increase at
       least as fast as than the square of the number of atoms involved. It is easy to run out of
       memory, in which case this tool will probably exit with a 'Segmentation fault'. You should
       consider carefully whether a reduced set of atoms will meet your needs for lower costs.

FILES

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -o eigenval.xvg Output
        xvgr/xmgr file

       -v eigenvec.trr Output
        Full precision trajectory: trr trj cpt

       -av average.pdb Output
        Structure file: gro g96 pdb etc.

       -l covar.log Output
        Log file

       -ascii covar.dat Output, Opt.
        Generic data file

       -xpm covar.xpm Output, Opt.
        X PixMap compatible matrix file

       -xpma covara.xpm Output, Opt.
        X PixMap compatible matrix file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        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

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -[no]fityes
        Fit to a reference structure

       -[no]refno
        Use the deviation from the conformation in the structure file instead of from the average

       -[no]mwano
        Mass-weighted covariance analysis

       -last int -1
        Last eigenvector to write away (-1 is till the last)

       -[no]pbcyes
        Apply corrections for periodic boundary conditions

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                          Mon 2 Dec 2013                               g_covar(1)