Provided by: gromacs-data_4.6.5-1build1_all bug


       g_rotmat - plots the rotation matrix for fitting to a reference structure

       VERSION 4.6.5


       g_rotmat -f traj.xtc -s topol.tpr -n index.ndx -o rotmat.xvg -[no]h -[no]version -nice int
       -b time -e time -dt time -[no]w -xvg enum -ref enum -skip int -[no]fitxy -[no]mw


        g_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  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

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


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -o rotmat.xvg Output
        xvgr/xmgr file


        Print help info and quit

        Print version info and quit

       -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)

        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -ref enum none
        Determine the optimal reference structure:  none,  xyz or  xy

       -skip int 1
        Use every nr-th frame for  -ref

        Fit the x/y rotation before determining the rotation

        Use mass weighted fitting



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                              g_rotmat(1)