NAME

       gmx-rotmat - Plot the rotation matrix for fitting to a reference structure

SYNOPSIS

          gmx rotmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                     [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
                     [-[no]w] [-xvg <enum>] [-ref <enum>] [-skip <int>]
                     [-[no]fitxy] [-[no]mw]

DESCRIPTION

       gmx  rotmat  plots  the  rotation matrix required for least squares fitting a conformation
       onto the reference conformation provided with -s. Translation is removed  before  fitting.
       The output are the three vectors that give the new directions of the x, y and z directions
       of the reference conformation, for example: (zx,zy,zz) is the orientation of the reference
       z-axis in the trajectory frame.

       This  tool  is  useful  for, for instance, determining the orientation of a molecule at an
       interface, possibly on a trajectory produced with gmx trjconv -fit rotxy+transxy to remove
       the rotation in the x-y plane.

       Option  -ref  determines a reference structure for fitting, instead of using the structure
       from -s. The structure with the lowest sum of RMSD's to  all  other  structures  is  used.
       Since  the  computational  cost  of  this procedure grows with the square of the number of
       frames, the -skip option can be useful. A full fit or only a fit in the x-y plane  can  be
       performed.

       Option -fitxy fits in the x-y plane before determining the rotation matrix.

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>] (rotmat.xvg)
              xvgr/xmgr 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)

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

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

       -ref <enum> (none)
              Determine the optimal reference structure: none, xyz, xy

       -skip <int> (1)
              Use every nr-th frame for -ref

       -[no]fitxy (no)
              Fit the x/y rotation before determining the rotation

       -[no]mw (yes)
              Use mass weighted fitting

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2024, GROMACS development team