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NAME

       g_covar - calculates and diagonalizes the covariance matrix

       VERSION 4.0.1

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 -nice int -b time -e time -dt time
       -tu enum -[no]xvgr -[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.

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

       -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

       -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:  ps,  fs,  ns,  us,  ms or  s

       -[no]xvgryes
        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -[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/>.

                                Thu 16 Oct 2008                     g_covar(1)