NAME

       gmx-covar - Calculate and diagonalize the covariance matrix

SYNOPSIS

          gmx covar [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                    [-o [<.xvg>]] [-v [<.trr/.cpt/...>]]
                    [-av [<.gro/.g96/...>]] [-l [<.log>]] [-ascii [<.dat>]]
                    [-xpm [<.xpm>]] [-xpma [<.xpm>]] [-b <time>] [-e <time>]
                    [-dt <time>] [-tu <enum>] [-xvg <enum>] [-[no]fit]
                    [-[no]ref] [-[no]mwa] [-last <int>] [-[no]pbc]

DESCRIPTION

       gmx  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 and eigenvalue as  step
       number and timestamp, respectively.

       The eigenvectors can be analyzed with gmx 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.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -o [<.xvg>] (eigenval.xvg)
              xvgr/xmgr file

       -v [<.trr/.cpt/...>] (eigenvec.trr)
              Full precision trajectory: trr cpt tng

       -av [<.gro/.g96/...>] (average.pdb)
              Structure file: gro g96 pdb brk ent esp

       -l [<.log>] (covar.log)
              Log file

       -ascii [<.dat>] (covar.dat) (Optional)
              Generic data file

       -xpm [<.xpm>] (covar.xpm) (Optional)
              X PixMap compatible matrix file

       -xpma [<.xpm>] (covara.xpm) (Optional)
              X PixMap compatible matrix file

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -[no]fit (yes)
              Fit to a reference structure

       -[no]ref (no)
              Use the deviation from the conformation in the structure file instead of  from  the
              average

       -[no]mwa (no)
              Mass-weighted covariance analysis

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

       -[no]pbc (yes)
              Apply corrections for periodic boundary conditions

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2023, GROMACS development team