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

2023.3                                            Oct 19, 2023                                      GMX-COVAR(1)