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gmx-covar(1)                    GROMACS Manual                    gmx-covar(1)

NAME
       gmx-covar - Calculate and diagonalize the covariance matrix

SYNOPSIS
       gmx covar [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
                 [-n [<.ndx>]] [-o [<.xvg>]] [-v [<.trr/.cpt/...>]]
                 [-av [<.gro/.g96/...>]] [-l [<.log>]] [-ascii [<.dat>]]
                 [-xpm [<.xpm>]] [-xpma [<.xpm>]] [-nice <int>] [-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 as
       timestamp.

       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 and output files:

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

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

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

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

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

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

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

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

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

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

       Other options:

       -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, 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
       gromacs(7)

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

VERSION 5.0.6                                                     gmx-covar(1)