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)