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

       2023, GROMACS development team

2023.3                                            Oct 19, 2023                                     GMX-ROTMAT(1)